Before European settlers arrived, Kingston was within the tribal homeland of the Wampanoag people. Several years before the Mayflower had landed in Plymouth, during the Native American epidemic of 1616 to 1619, the Wampanoag population was severely damaged from a rapidly spreading pandemics due to earlier contacts with Europeans. Several ancient Native American burial sites have been located within the borders of Kingston.

Originally part of Plymouth, Kingston was first settled by Europeans shortly after the landing of the Pilgrims at Plymouth Rock in 1620. It was settled once more in 1635. During 1675, several bloody battles during King Philip's War are believed to have occurred within Kingston's borders and the residence of Governor Bradford, which is now part of Kingston, was raided by Wampanoag warriors.

In 1685, the area was placed within the boundaries of Plymouth County and for a brief time, between 1686 and 1689, the borders of Kingston were within the Dominion of New England.

Kingston was first established as Plymouth's northern precinct in 1717 upon the creation of First Parish Kingston, now a Unitarian Universalist church in the town's center. Kingston was incorporated as a distinct town on June 16, 1726, following a tax dispute between the residents of north and south Plymouth, when the parish was known as the upper class portion of Plymouth. Kingston's borders were carved out of neighboring towns Plymouth, Duxbury, Plympton and Pembroke, all of which were incorporated before Kingston.

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