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Welcome to Flagship Inn, a Boothbay Harbor Inn

Welcome to the finest choice in Boothbay Harbor, Maine lodging. The pet-friendly Flagship Inn invites you to relax in some of the Boothbay Harbor Region's most comfortable and reasonable accommodations, all guaranteed by AAA and Mobil guide ratings. "Best value" is how our guests describe us! We are locally owned and operated, which allows us to offer the exceptional service of a small inn with the modern amenities of a chain hotel. Our lodging in Boothbay Harbor, Maine is less than a mile from the Atlantic oceanfront and from all downtown Boothbay Harbor has to offer.

The Flagship Inn features 82 modern guest rooms complete with double or king size beds to make your stay a comfortable one. Also enjoy our spacious Family Suites for larger families or spacious extended-stay accommodations.

Compare Us to Boothbay Harbor, Maine Hotels

Our services and amenities at the Flagship Inn are among the very finest. All of our rooms feature free Internet access, Cable TV with HBO, Free long distance calling, electronic key locks, mini fridges, hairdryers, irons, and ironing boards. Enjoy our complimentary Continental breakfast, or join us for coffee and a newspaper in our lobby while our friendly and knowledgeable staff helps you plan your day. Your car is just outside in our ample parking lot, or you can leave it and take a ride around downtown on the seasonal trolley. The Flagship Inn also features a large outdoor heated pool and spa for you to enjoy throughout the late spring and summer season.

The Inn is the perfect place to wrap yourself in the charm of Boothbay Harbor. Whether a family vacation, casual getaway, or comfortable home base, your experience at the Inn will bring you back time and time again. For complete information on our lodging in Boothbay Harbor, Maine please feel free to contact us at (800) 660-5094.

For Labor Day Weekend, the Flagship Inn is participating in Harbor Fest Activities.  Friday night there will be a Trolley Stop here on the "Harbor Crawl".  Saturday at 2:00 PM our staff will be serving Chili for the Chili/Chowder contest at the Pool.  We will have live music with Timothy Gurshin from 2:00 to 4:00 PM.  Come and join us! 


» Boothbay's 250th Anniversary Celebration
8/14/2014 from Boothbay Harbor Hotel
Boothbay's 250th Anniversary Celebration will include many events.  Join us at the Flagship Inn for a great time.  There will will fireworks! Friday, Aug. 22 – Seafood Festival on the Common. Join the fun on the Boothbay Common...

» Day Out with Thomas: The Thrill of the Ride Tour 2014
8/4/2014 from Boothbay Harbor Hotel
When Thomas arrives at Boothbay for the Day Out with Thomas™: The Thrill of the Ride Tour 2014, he will not only take his fans for a ride, but also talk to them for the very first time on the tour!    Day Out with Thomas: The T...


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"Accommodations are convenient, economical, friendly and clean."