Marathon Boot Key Harbor Hotels: 2026 Limited-Time Hotel Deals @Expedia

Three white herons standing among green foliage.

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Our top choices for Boot Key Harbor hotels

A marina with several docked boats and a row of small, white cabins with blue roofs.

A modern kitchen with white cabinets, a microwave, and a dining area with a table and chairs.

A compact bedroom with two beds, a small bathroom, and a view of the outdoors.

A waterfront property with floating houses connected by a wooden dock.

1. Yacht Haven Marina

2.2 km from Boot Key Harbor

Clara

HK$691

HK$1,880 total

includes taxes & fees

14 Sept - 15 Sept

A coastal landscape with clear turquoise waters and a dense tree line under a bright blue sky with scattered clouds.

A coastal area with a marina, boats, and a small island with buildings.

A waterfront dock with boats and a sunset.

A beach with a wooden pier, palm trees, and a clear blue sky.

2. Captain Pips Marina & Hideaway

1.2 km from Boot Key Harbor

Amy

HK$726

HK$1,038 total

includes taxes & fees

12 Sept - 13 Sept

An aerial view of a resort with a central pool, multiple buildings, and a beach area with sun loungers.

A beach with white chairs and kayaks, palm trees, and a clear view of the ocean.

A bar area with wooden chairs, a bar counter, and a variety of bottles and glasses.

An aerial view of a resort with a large building, a beach, and a pier in the background.

3. Isla Bella Beach Resort & Spa

2.4 km from Boot Key Harbor

Silvia

HK$1,616

HK$2,287 total

includes taxes & fees

13 Sept - 14 Sept

A resort with a pool, lounge chairs, and a view of the ocean.

A deck with tables and chairs, overlooking a calm body of water and palm trees.

A hammock tied between palm trees on a rocky beach with a view of the sea.

A dock with boats, a wooden pier, and a distant shoreline with palm trees.

4. Bluegreen Vacations Hammocks at Marathon, Ascend Collection Resort

1.2 km from Boot Key Harbor

Anthony

HK$993

HK$1,338 total

includes taxes & fees

30 Sept - 1 Oct

Two hammocks on a sandy beach with a clear blue sky and turquoise water.

A bar area with a view of the ocean, bar stools, umbrellas, and a variety of bottles.

An aerial view of a coastal resort with a marina, palm trees, and a large building complex.

A clear blue pool with white lounge chairs and palm trees, overlooking a calm sea.

5. Courtyard by Marriott Faro Blanco Resort, Marathon Florida Keys

0.8 km from Boot Key Harbor

Evelyn

HK$1,123

HK$1,572 total

includes taxes & fees

22 Sept - 23 Sept

A modern kitchen with white cabinets and a built-in microwave.

6. Aqua Lodges at 47th Street Gulfside

1.9 km from Boot Key Harbor

Lauren

HK$1,052

HK$2,286 total

includes taxes & fees

7 Sept - 8 Sept

A marina with boats docked, a lighthouse, and a resort with outdoor seating.

A bar area with a long counter, multiple bar stools, and a view of the marina with boats and palm trees.

A spacious lobby with a central round table, surrounded by wicker chairs, large potted plants, and decorative lanterns.

A room with two sofas, a round coffee table, and a small side table with a vase.

7. Faro Blanco Resort Marathon Florida Keys, Curio by Hilton

1 km from Boot Key Harbor

Patricia

HK$1,151

HK$1,590 total

includes taxes & fees

22 Sept - 23 Sept

An outdoor seating area with wicker furniture and cushions, a thatched-roof structure, and lush greenery.

A thatched-roof bar area with a large island counter, bar stools, and a television screen.

A food truck parked in a lush garden with a brick pathway, surrounded by various plants and a white fence.

A bedroom with a bed, bedside tables, a TV, and a sliding glass door to the outside.

8. Tropical Cottages

2.9 km from Boot Key Harbor

Natasha

HK$745

HK$838 total

includes taxes & fees

8 Sept - 9 Sept

A nighttime pool area with a clear view of the pool, surrounding palm trees, and a building with a sign.

A buffet setup with various food items and condiments.

A hotel entrance with a covered walkway, palm trees, and a clear blue sky.

A waterfront property with a swimming pool, palm trees, and a white fence.

9. Skipjack Resort & Marina

1.7 km from Boot Key Harbor

Justin

HK$1,122

HK$1,580 total

includes taxes & fees

8 Sept - 9 Sept

Three Adirondack chairs on a sandy beach with a view of the ocean and a clear sky.

A beach with lounge chairs, palm trees, and a string of lights.

A marina with boats docked, a dock extending into calm waters, and a small island with palm trees.

An aerial view of a marina with multiple boats docked, surrounded by a sandy beach and palm trees.

10. Banana Bay Resort & Marina

1.6 km from Boot Key Harbor

michael

HK$793

HK$1,201 total

includes taxes & fees

7 Sept - 8 Sept

A swimming pool surrounded by palm trees and lounge chairs.

A spacious living room with a wooden coffee table, a striped sofa, and a television on a wooden cabinet.

A beach scene with a wooden deck, palm trees, and a gazebo-like structure.

A wooden deck with blue chairs overlooking a beach with palm trees and the ocean.

11. Tranquility Bay Beachfront Hotel and Resort

0.7 km from Boot Key Harbor

Stuart

HK$1,499

HK$2,188 total

includes taxes & fees

27 Sept - 28 Sept

A hammock on a sandy beach with palm trees, a pool, and lounge chairs in the background.

A view from a balcony overlooking a beach with palm trees, a wooden deck, and a blue picnic table.

A pool with a view of the ocean and beach chairs.

A wooden pier leading to a dock with boats, a clear sky, and calm water.

12. Seascape Resort & Marina

4.1 km from Boot Key Harbor

Sujoy

HK$803

HK$1,295 total

includes taxes & fees

14 Sept - 15 Sept

A wooden deck with a pool and chairs overlooking a beach with palm trees.

A bar area with stools, a counter, and hanging lanterns.

A beach with a wooden walkway leading to the water, palm trees, and a clear sky.

A pool area with palm trees and a view of the ocean.

13. Grassy Flats Resort & Beach Club

15.6 km from Boot Key Harbor

Tiffany

HK$1,223

HK$1,753 total

includes taxes & fees

14 Sept - 15 Sept

A bar area with a long counter, bar stools, and a view of the water.

A balcony with a view of the ocean, a round table, and two chairs.

A balcony with a view of a body of water, a pool, and outdoor seating.

A waterfront property with a large building, a smaller structure with a thatched roof, and several boats docked.

14. Fairfield Inn & Suites by Marriott Marathon Florida Keys

8.3 km from Boot Key Harbor

Lizabell

HK$1,051

HK$1,183 total

includes taxes & fees

13 Sept - 14 Sept

Three colorful drinks on a table with a thatched roof and outdoor seating.

A bar area with wicker chairs and a thatched roof, overlooking a body of water with boats.

A modern living room with a large sectional sofa, a flat-screen TV, and a view of the sea through large windows.

A modern kitchen with a central island, various appliances, and hanging pendant lights.

15. Hampton Inn Marathon - Florida Keys

8.5 km from Boot Key Harbor

Annie

HK$1,022

HK$1,150 total

includes taxes & fees

27 Sept - 28 Sept

A pool area with lounge chairs and umbrellas, a thatched-roof structure, and a view of the ocean.

A covered outdoor seating area with a view of the ocean, a small table, and two chairs with cushions.

A spacious living area with a view of the ocean, a balcony with a pool, and a staircase leading to another level.

A beach with a palm tree, clear blue water, and a bridge in the distance.

16. Glunz Ocean Beach Hotel & Resort

8.3 km from Boot Key Harbor

Erica

HK$1,325

HK$1,828 total

includes taxes & fees

9 Sept - 10 Sept

A covered outdoor area with a view of a pool and palm trees.

A hotel room with two beds, white bedding, and a blue accent.

A covered patio with a round table and chairs, large windows, and a view of a street and greenery.

A reception desk with a marble countertop, a Toshiba laptop, a vase with white flowers, and a sign indicating an office.

17. Kingsail Resort

3.6 km from Boot Key Harbor

oldrich

HK$551

HK$620 total

includes taxes & fees

17 Sept - 18 Sept

A marina with a dock, a boat, and a row of buildings with large windows.

A bedroom with a bed, a dresser, a large window, and a painting of a sunset over the ocean.

A pool area with lounge chairs and umbrellas, surrounded by palm trees and a white fence.

A two-story beachfront hotel with a wooden deck, palm trees, and a clear sky.

18. Coconut Cay Resort & Marina

3.7 km from Boot Key Harbor

Huy

HK$537

HK$685 total

includes taxes & fees

22 Sept - 23 Sept

A tropical resort with a swimming pool, palm trees, and a view of the ocean.

A beach view with palm trees, a hammock, and a chair by the water.

An aerial view of a resort with a swimming pool, palm trees, and a beach area.

A bright kitchen with white cabinets and a microwave, a glass table with white chairs, and a view of palm trees and the ocean through large windows.

19. Gulf View Waterfront Resort

16.4 km from Boot Key Harbor

Sonja L

HK$683

HK$768 total

includes taxes & fees

8 Sept - 9 Sept

A wooden deck with two chairs and a table, overlooking a beach with palm trees and the ocean.

A table with breakfast items and a view of the beach.

A beach with lounge chairs and umbrellas, palm trees, and a building with balconies.

A swimming pool with a hot tub, palm trees, and a building with a staircase.

20. Rainbow Bend Resort

15 km from Boot Key Harbor

Adam

HK$641

HK$1,074 total

includes taxes & fees

14 Sept - 15 Sept

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Compare popular hotels close to Boot Key Harbor

Property	Property class	Guest rating
Yacht Haven Marina	9.8 Exceptional 355 reviews	View
Captain Pips Marina & Hideaway	9.0 Wonderful 1,004 reviews	View
Isla Bella Beach Resort & Spa	9.2 Wonderful 1,258 reviews	View
Bluegreen Vacations Hammocks at Marathon, Ascend Collection Resort	9.2 Wonderful 144 reviews	View
Courtyard by Marriott Faro Blanco Resort, Marathon Florida Keys	9.0 Wonderful 1,002 reviews	View

Top Boot Key Harbor Hotel Reviews

Isla Bella Beach Resort & Spa

8/10 Good

"Pros -beautiful resort -very nice pools -marketplace is great and convenient -felt very safe -1 bedroom was very big -2 bathrooms was great -across the street from the old 7 mile bridge with a 5 mile round trip walk to Pigeon Key -easy pick up by boat from marina Cons -bed was extremely hard for me -very loud due to the walkways being wood -right next to a laundry so we started hearing lots of loud noise next door at 6:45am which didn't stop until 7pm -only 40% occupancy when we were there and our room was next to the laundry and then a family with 3 little kids were next to us on the second day. -walls are paper thin. Sounded like the kids were in the room with us. -so close I could smell the Doritos they were eating on their balcony. **Next time we will get a 2 bedroom and use the bedroom in the back so we don't hear the noise. **Upon checkout we were asked how our stay was. I told them about the noise and was offered free parking for our 3 nights stay. I feel that was a fair compensation."

Yacht Haven Marina

10/10 Excellent

"The staff was very friendly and helpful. We will 100% go back."

Tranquility Bay Beachfront Hotel and Resort

10/10 Excellent

"The property is well kept and extremely clean. One of the cleanest I have ever seen to my delight. The restaurant's menu was amazing and the food fresh and delicious. The only thing I wasn't happy was the fees and extra expenses that appeared out of the blue at the check out...In my opinion those things should have been included in the reservation. Overall the experience was outstanding."

Deep Water Canal, Swim Spa Pool, Kayaks, Walk to Ocean Front Bars & Restaurants!

8/10 Good

"Very well equipped house just need a couple of improvements like new houses and water connections on front of the house for washing the boat trailer , in general is a great place and location."

Captain Pips Marina & Hideaway

10/10 Excellent

"Parking was limited, but I was there during the off season, so it was easy to secure a good space"

Banana Bay Resort & Marina

8/10 Good

"solid hotel, nice rooms breakfast could be better"

4BR 3BATH, HEATED POOL, DOCK, Condé Nast Traveler's Best Marathon Rental

10/10 Excellent

"Andy was one of the best hosts we've had. He was quick to respond to any communiations and was friendly and welcoming. He was able to address some concerns that were out of his control with alternative solutions which is rare to find. Everything was clean and bright throughout the space. The pool was refreshing after a long day out on the water. We absolutely loved the kitchen with all the space for multiple chefs at once. The covering on the top floor terrace as shown in the photos was not there but moved to the bottom patio, but since it was hot out, we took advantage of the terrace inthe evening instead for sunsets and stars. When we plan on returning to Marathon, we will definitley see if this rental is available as the location was fantastic and just a short way to the seven mile bridge."

Skipjack Resort & Marina

10/10 Excellent

"Great spot"

Waterfront Luxury Living Inside & Out, Gulf View, On the Water!!

10/10 Excellent

"If you're looking for a home away from home, this is it! The property is an amazing paradise. Boat slips available, plenty of water views, a great area for enjoying a night of grilling out by the water, and a refreshing pool to fight the Florida heat! The owner lives above the rental space, and this is no way a detriment. Muffet is incredibly kind and helpful. It was difficult saying goodbye at the end of our stay! We loved watching the parrotfish and lobsters swimming right off the the dock. This was by far our favorite experience we've had in the Keys, and we can't wait to return."

Other attractions near Boot Key Harbor

The Turtle Hospital

9.2/10 (946 reviews)

Explore the campus of The Turtle Hospital as part of your travels around Marathon. Stroll along the area's beautiful beaches or simply savour its seafood restaurants.

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A golf course with a curved path, palm trees, and a clear blue sky.

Florida Keys Country Club

8.2/10 (111 reviews)

Play a round of golf in Marathon at Florida Keys Country Club, and enjoy other activities such as running. Stroll along the area's marina or simply savour its seafood restaurants.

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A sailboat named 'Soundwave' docked at a calm harbor with clear blue water, surrounded by a sandy beach and lush greenery.

Sombrero Beach

9.0/10 (2,464 reviews)

Play beach games; go swimming, kayaking or snorkeling; and lounge in the sun at one of Marathon’s most visited beaches.

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A tropical beach with green vegetation and clear blue water.

Crane Point Museum and Nature Center

8.6/10 (54 reviews)

You can spend an afternoon exploring the galleries in Crane Point Museum and Nature Center in Marathon. Discover the area's beautiful sunsets or seek out its jogging trails.

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A tall red lighthouse on a pier in the ocean.

Vaca Key

8.8/10 (411 reviews)

Commune with nature and explore the great outdoors at Vaca Key during your travels in Marathon. Stroll along the seaside or discover the area's beautiful sunsets.

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A bridge over turquoise water with a clear sky.

Seven Mile Bridge

9.4/10 (3,266 reviews)

Walk, jog, cycle or drive across one of the longest bridges in North America to take in the scenic ocean views it provides.

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Shady Palm Art Gallery

You can spend time browsing the exhibits at Shady Palm Art Gallery during your trip to Marathon. Stroll along the area's marina or simply savour its seafood restaurants.

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Marathon Air Museum

You can spend an afternoon browsing the exhibits at Marathon Air Museum during your travels in Marathon.

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Frequently asked questions

What's the area like around Boot Key Harbor?

Boot Key Harbor is located in Marathon. Travellers love the area for its beautiful beaches, top seafood restaurants and dolphin watching opportunities. If you're looking for a convenient place to stay, take a look at the 202 hotels and other accommodation options you'll find within a mile.

Where is the best place to stay near Boot Key Harbor?

Tranquility Bay Beachfront Hotel and Resort is one of the top choices for your stay based on our traveller data, and this hotel offers 3 outdoor pools and a private beach. It's located just a short 0.4 mi (0.7 km) from Boot Key Harbor. Other good options within a short distance include Faro Blanco Resort Marathon Florida Keys, Curio by Hilton and Courtyard by Marriott Faro Blanco Resort, Marathon Florida Keys.

How many hotels will I find close to Boot Key Harbor?

Expedia has 202 hotels and other accommodation options within a mile from Boot Key Harbor.

If I need to cancel the hotel reservation for my stay near Boot Key Harbor, will I receive a refund?

Yes! Most hotel reservations are refundable provided that you cancel before the accommodation's cancellation deadline, which in most cases is within 24 or 48 hours of your arrival date. If you have a reservation that's non-refundable, it might still be possible to cancel it and be given a refund within a 24-hour period of your booking. Add dates, click "Search", then filter by "fully refundable" to review top deals close to Boot Key Harbor.

What can I see and do near Boot Key Harbor?

Lounge by the water at Sombrero Beach and Sunset Park Beach. Attractions like Shady Palm Art Gallery and Crane Point Museum and Nature Center highlight the local culture. Explore nature at Vaca Key and Pigeon Key.

Marathon Boot Key Harbor Hotels

Change your mind

Treat yourself

Be picky

Check prices for these dates

Filter by

Star rating

Guest rating

Our top choices for Boot Key Harbor hotels

1. Yacht Haven Marina

2. Captain Pips Marina & Hideaway

3. Isla Bella Beach Resort & Spa

4. Bluegreen Vacations Hammocks at Marathon, Ascend Collection Resort

5. Courtyard by Marriott Faro Blanco Resort, Marathon Florida Keys

6. Aqua Lodges at 47th Street Gulfside

7. Faro Blanco Resort Marathon Florida Keys, Curio by Hilton

8. Tropical Cottages

9. Skipjack Resort & Marina

10. Banana Bay Resort & Marina

11. Tranquility Bay Beachfront Hotel and Resort

12. Seascape Resort & Marina

13. Grassy Flats Resort & Beach Club

14. Fairfield Inn & Suites by Marriott Marathon Florida Keys

15. Hampton Inn Marathon - Florida Keys

16. Glunz Ocean Beach Hotel & Resort

17. Kingsail Resort

18. Coconut Cay Resort & Marina

19. Gulf View Waterfront Resort

20. Rainbow Bend Resort

Compare popular hotels close to Boot Key Harbor

Top Boot Key Harbor Hotel Reviews

Isla Bella Beach Resort & Spa

Yacht Haven Marina

Tranquility Bay Beachfront Hotel and Resort

Deep Water Canal, Swim Spa Pool, Kayaks, Walk to Ocean Front Bars & Restaurants!

Captain Pips Marina & Hideaway

Banana Bay Resort & Marina

4BR 3BATH, HEATED POOL, DOCK, Condé Nast Traveler's Best Marathon Rental

Skipjack Resort & Marina

Waterfront Luxury Living Inside & Out, Gulf View, On the Water!!

Other attractions near Boot Key Harbor

The Turtle Hospital

Florida Keys Country Club

Sombrero Beach

Crane Point Museum and Nature Center

Vaca Key

Seven Mile Bridge

Shady Palm Art Gallery

Marathon Air Museum

Frequently asked questions