Long before English fishermen and fur traders began frequenting the waters of Monhegan, Damariscove and Pemaquid, Native Americans inhabited the area. As recently as the first decade of the 17th century, there was a sizable Wabanaki settlement on the Pemaquid Peninsula. However, by the time a year-round English settlement was established in the 1620's, the area's Indian population was reduced to a fraction of its previous numbers.

In 1631 two merchants from Bristol, England became patent-holding proprietors of Pemaquid, acquiring 12,000 acres plus 100 acres for every settler they brought over from England. By 1665, there were approximately 30 houses existing at Colonial Pemaquid, and by the early 1670's Pemaquid may have had a population of between 150 and 200 people. The settlement, however, was part of an unstable frontier on the northern fringe of British territory that was also claimed by the French.

As a point of contact and conflict with the French and the Native Americans who often joined them, Pemaquid was subject to several devastations. The first occurred in 1676, when the Abenaki Indians burned the village during a King Philip's War regional uprising. Fort Charles, a wooden fortification, was constructed the following year, but it and the rebuilt village were demolished in a 1689 attack. In 1692 Fort William Henry, probably New England's first stone fortification, was erected by the Massachusetts Bay Colony. Within four years it too was leveled by the combined efforts of the French and Wabanakis, and the Pemaquid settlement was abandoned for 30 years.

In 1729 a British officer, Colonel David Dunbar (who bore the title Surveyor of His Majesty's Woods in American) built Fort Frederick on the ruins of Fort William Henry. Dunbar established a third settlement, laying out streets, framing 30 to 40 houses, and recruiting as many as 200 residents. However, when Dunbar's claim to the land was disputed by the Massachusetts government in 1732, he was forced to leave, and the community gradually dispersed. Fort Frederick was defended against several further French and/or Indian attacks, but was decommissioned in 1759. 

A few years later on the eve of the Revolutionary War as the risk of conflict between Europeans and Native Peoples became less frequent, focus began to shift from survival toward the creation of a new and independent nation - the United States of America.

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