About Us

At Flagship Inn & Suites in Boothbay Harbor, Maine, our number one priority is our guests. We know that you’re tired of being frustrated at having to choose between cost and comfort – and that’s why we’re here to help you be the hero of your coastal Maine getaway. We offer affordable accommodations with amazing service and comfort, making it easy to choose us as your home away from home for your vacation!

When you book a room with us, you’ll get more than just a bed to lay your head. You’ll experience…

Affordable Comfort & Service

We pride ourselves on attentive and hospitable service and comfort at an affordable cost. We love welcoming guests to Boothbay Harbor, sharing our favorite local attractions and destinations, and hearing about our guests’ amazing coastal Maine experiences.

Our heated outdoor pool, complimentary breakfast each morning, pet-friendly rooms, fresh baked cookies each afternoon, and family suites are often what draw guests in, but our seasoned staff and convenient location are what brings them back time and time again.

Locally owned and operated, our hotel in Boothbay Harbor is known for our friendly and attentive service. The majority of our staff have been with us for 15-20 years, and they are a big part of what makes our property so special. Their attention to guests’ details provides that “home away from home” feeling and they are always ready to serve!

Convenient Location

Our property is adjacent to the many walking trails at Penny Lake Preserve (connected by a footbridge) and just a 0.6 mile stroll down the roadside sidewalk to the water’s edge in the mouth of the harbor. If you’re traveling with kids or are a kid at heart, you’ll love the outdoor playground equipment and nearby sports fields and tennis courts.

Whether you’re visiting the Coastal Maine Botanical Gardens, looking forward to eating lobster at LobsterFest, or checking out all the boats at WindJammer or HarborFest, we’re here to welcome and serve you during your stay in Boothbay Harbor, Maine.

Amenities & Accommodations

It’s the little touches that will make your coastal Maine getaway stand out. That’s why we go the extra mile, providing affordable accommodations with service and amenities to increase your comfort during your stay at Flagship Inn & Suites.

Our award-winning Boothbay Harbor hotel offers 80+ rooms and is open year-round. Rooms range from standard double rooms to family suites and offer amenities such as cable TV with HBO, mini-fridges, and more.

Get the best rates on our rooms when you book direct through our website or call us at (207) 633-5094!

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All guests are invited to use our outdoor heated pool (seasonal), enjoy a complimentary continental breakfast (daily), and nibble on fresh-baked cookies (every day from 4-7 pm).

Flagship Inn & Suites is conveniently located in Boothbay Harbor, Maine, and has designated handicap accessible and pet-friendly rooms, is perfect for family vacations, romantic getaways, and business travels.

You can find a detailed list of all our accommodations here.

Awards & Affiliations

The greatest award we could receive at Flagship Inn & Suites is for a guest to trust us with their getaway or family vacation, leave us a review or comment card letting us know something specific about their stay experience, and for our satisfied guests to tell their friends and family about the hospitality they experienced at the Flagship Inn & Suites.


We’re here for you – to help you be the hero of your coastal Maine getaway. That’s why we pride ourselves on maintaining the rigorous standards for hospitality certifications:

  • AAA 2-Diamond property
  • TripAdvisor Certificate of Excellence
  • Platinum Green Leader on TripAdvisor

Other Awards & Recognition

And when other local Boothbay Harbor travel resources have good things to say about us, we know we’re doing our best to serve you well:

  • Downeast Dog News Magazine awarded us as the Best Pet-Friendly Hotel.
  • We stock our pet-friendly rooms with items from our partner, Two Salty Dogs Pet Outfitters, who was voted the best pet store in Maine.
  • We are proud members of the Maine Tourism Association, the Boothbay Harbor Chamber, the Boothbay Chamber, and Damariscotta Chamber.
  • In 2018, we even won first place in the lighting contest for businesses during Gardens Aglow!

Green Lodging on the Maine Coast

Because we want to be your home away from home for years to come, we promise to:

  • Adopt responsible practices regarding the environmental impacts of our hotel. We will continually review our ideas and plans for achieving our goal to protect our local environment.
  • We seek to reduce the impact we have on our planet by efficiently using resources, saving energy, reducing waste, and encouraging recycling.

It’s important to us to be an environmentally-friendly hotel, so we’re doing things to help preserve our natural environment:

  • We have recently installed a large Solar Panel system, to reduce the load on the Electrical Grid.
  • Our outdoor pool uses a natural salt to sanitize the water with no harsh chemicals.
  • Our sheet and towel programs help to use less water & electricity.
  • We recycle plastic, glass, cardboard and paper products from our breakfast and guest rooms.
  • Whenever possible, we are using eco-friendly cleaning chemicals in our rooms and public areas.
  • Our natural marshland is surrounded by indigenous plants, which assist with run-off.
  • All of our bathroom fixtures are low-water flow to help preserve water.
  • All of our light bulbs have been changed to LED lighting, to help save electricity.

Our Sister Properties – Glen Cove Inn & Suites and The Country Inn

We have two sister properties located just up the coast in the Camden/Rockland/Rockport area. Glen Cove Inn and Suites is a traditional-style, seasonal, mid-Maine motel with 36 rooms near Rockland featuring a better-than-continental breakfast, heated outdoor pool, and friendly staff. The Country Inn at Camden Rockport includes 36 guest rooms in the main house and an additional 11 seasonal cottages on the property. It features a country-style breakfast buffet, afternoon treats, an indoor pool and spa, and year-round accommodations.


Let us help make you the hero of your Boothbay Harbor vacation. Book direct with us, and we’ll save you money without skipping on comfort or service!