Renamed Boothbay in 1842, the harbor continued to develop as a fishing center. In bad weather, it could hold at a time between 400 and 500 vessels, often Friendship Sloops, seeking shelter. By 1881, it had a fishery and fish oil company, an ice company, two marine railways, a fertilizer manufacturer, and a factory for canning lobsters. On February 16, 1889, the community was set off from Boothbay and incorporated as the town of Boothbay Harbor.[6] Frank L. Sample shipyard at Boothbay Harbor built minesweepers for the United States Navy during World War II and into the 1950s.[7]

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