
Boutique hotels in Marathon
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Top-rated boutique hotels in Marathon
Guests agree: these boutique hotels are highly rated for location, cleanliness and more.

Conch Key Villas #2 Peaceful waterfront lodging
Studio Two's waterfront rental is located on the ground level. Each unit comes with a boat slip and parking for your trailer. We can handle boats up to 25’. There is a boat ramp just 2 blocks away. We provide outside table and chairs, and just around the corner, the barbecue grill. Our accommodations include king bed, living and dining area, futon, polished terrazzo floors, waterfront patio, literally 6 feet from the water, full size and equipped kitchens, A/C and cable TV, DVD and Wi-Fi.

Conch House 2 Bedroom King ADA at Grassy Flats
Enjoy a Grassy Key Getaway in our spacious two-bedroom suite! With private bedrooms that each have one king bed, you can comfortably accommodate up to four guests, with extra room to store your water sports gear. A fully equipped kitchen makes it ideal for cooking family meals and dining comfortably in the suite. This suite has an ADA accessible bathroom with a walk-in shower. This unit has two king beds, 2.5 bathrooms, a full kitchen, living/dining area, and two private balconies.

Large House w/ FREE Sailboat, Kayaks, Snorkel etc
The Main House is a cottage at Key Largo Cottages. We are located on the bay side of Key Largo near some of the best dive/snorkel sites, island excursions, bars, restaurants, & the Everglades. Experience water fun! A stay in one of our cottages comes with unlimited use of our kayaks, canoes, paddle boards, snorkel gear, fishing gear, &, of course, the use of one of our 22' sailboats, if you have recent sailing experience on keel boats! You won't find a better deal in the Keys!

Conch Key Villas #1. Fun, fishing & great sunsets
Studio One's waterfront rental is located on the ground level. Our units differ vastly from other Florida Keys lodgings because our property is right on Florida Bay. If you trailer your boat, the dockage is a few feet from the back door. Our docks can handle boats up to 25’ and you can park your trailer in our front lot. There is a boat ramp just two blocks away. Studio 1 can sleep 2 adults and one child (up to 12 years). We have a king size bed and a futon.

Conch House 3 Bedroom Suite at Grassy Flats Resort
Our spacious three-bedroom suites offer three private rooms with one king-sized bed, two queen-sized beds, and two full baths, with extra room for all of your water sports gear. These deluxe suites can comfortably accommodate up to six people with double occupancy per room, so grab some friends and come soak up the vibes! A full kitchen gives you all the tools and space you need for families and friends to enjoy meals together.

Conch House 2 Bedroom Suite at Grassy Flats Resort
Enjoy a Grassy Key Getaway in our spacious two-bedroom suite! With private bedrooms that each have one queen bed, you can comfortably accommodate up to four guests, with extra room to store your water sports gear. A fully equipped kitchen makes it ideal for cooking family meals and dining comfortably in the suite. This unit has two queen beds, 1.5 bathrooms, a full kitchen, living/dining area, and two private balconies.

Wreckers House Double Queen Room - Adults Only
Adults-only building, available for guests ages 21+ only. Thoughtfully furnished with mixed metals and woods, the Wreckers House tells the story of ships and their crews of "wreckers" who once salvaged goods from the sunken ships in the Florida Keys. Enjoy a sunrise view and an ocean breeze from your private balcony that overlooks the pool and the Atlantic. This room has a mini fridge and an espresso machine.

Wreckers House King Room - Adults Only
Adults-only building for guests ages 21+ only. Thoughtfully furnished with mixed metals and woods, the Wreckers House tells the story of ships and their crews of "wreckers" who once salvaged goods from the sunken ships in the Florida Keys. Enjoy a sunrise view and an ocean breeze from your private balcony that overlooks the pool and the Atlantic. This room has a mini fridge and an espresso machine.

Family Oasis Escape | Plush King Bed + Bunk Bed
Gather the crew in the Family Oasis—a bright, roomy hideaway where bunk beds delight the kids and a plush king bed welcomes parents. Ideal for up to five guests, this relaxing space blends laid-back comfort with family-ready convenience. Located in Hawks Cay Resort, enjoy a full day of waterside fun, unwind in your oversized room, and let island time set the pace for your unforgettable stay.

Conch Key Villas Unit #4- Overlooking Florida Bay
This upstairs unit is fully remodeled with new kitchen and bath. It has all new modern appliances with icemaker and filtered water as well as pots, pans, dishes, drip coffee maker, Keurig. USB chargers, smart TV and other modern conveniences. This unit has a private balcony with fantastic views of Florida Bay and the best sunsets in all the Keys.

Humidor House King Room - Adults Only
Adults-only building, available for guests ages 21+ only. Decorated with an ode to Caribbean cigar making, the Humidor House has a cozy, sophisticated feel. With a private oceanfront balcony that's just steps away from the water, it’s the perfect getaway for solo travelers and couples alike. This room has a mini fridge and an espresso machine.

Marathon Oceanfront Suite | Balcony + 2 Luxe Baths
Experience breathtaking oceanfront luxury in the Oceanfront Balcony | 2BR 2Qns room. Featuring a king bed, two queen beds, and two deluxe bathrooms, this spacious retreat is perfect for families or groups. Relax on the private oceanview terrace, enjoy modern comforts, and indulge in five pools, beachside dining, and endless adventures.
Popular amenities for Marathon boutique hotels
Family-friendly boutique hotels

2BR Unit, Enjoy Paradise with On-site Pools!

Marathon Beachfront | 2Kings, Veranda + 2LuxeBaths

Parrot Key, Garden Villa 2 Kings, 1 Queen

Partial Water View Two Bedroom Suite w/Living Room

Parrot Key, Garden 2 Bedroom Suite w/ Living Room

Waterfront Two Bedroom Suite
Boutique hotels with a patio

Conch Key Villas #1. Fun, fishing & great sunsets

Conch Key Villas #2 Peaceful waterfront lodging

Resort View Family Suite

Wreckers House Double Queen Room - Adults Only

Galleon King Suite - Adults Only
Other boutique hotel holiday rentals

Poolside Double Queen | Duck Key | No Hidden Fee

Duck Key | King ADA w/ Balcony | No Hidden Fee

Marathon Beachfront | 2 Queens + Veranda

Marathon Oceanfront | 2 King Beds + Balcony

Marathon Beachfront Suite | 1BR Veranda +Luxe Bath

ADA Family Room | Resort Perks | No Hidden Fee

Comfy Double Queen | Garden View | No Hidden Fee

Marathon Oceanfront Suite | Balcony + Dog-Friendly
Quick stats about boutique hotels in Marathon

Total holiday rentals
Explore 30 holiday rentals in Marathon

Nightly prices starting at
Marathon holiday rentals start at £178 per night before taxes and fees

Verified guest reviews
Over 1,490 verified reviews to help you choose

Pet-friendly holiday rentals
Find 10 rentals that welcome pets

Holiday rentals with a pool
30 properties feature pools

Rentals with dedicated workspaces
10 properties have a dedicated workspace

Wifi availability
30 of Marathon holiday rentals include wifi access

Popular amenities for guests
Guests love Kitchen, Wifi and Pool across Marathon rentals

4.7 Average rating
Marathon stays receive an average rating of 4.7 out of 5 from guests
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- Everglades National Park
- Sombrero Beach
- Smathers Beach
- Calusa Beach & Loggerhead Beach
- Sea Oats Beach
- Long Beach
- Conch Key
- Bahia Honda State Park
- Theater of the Sea
- Fort Zachary Taylor Historic State Park
- Key Largo Kampground And Marina
- Seven Mile Bridge
- Calusa Campground
- Ernest Hemingway Home & Museum
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- Sunset Park
- Dolphin Research Center
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- Founder's Park
- Southernmost Point
- Key West Butterfly & Nature Conservatory
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