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.