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Fairfield County was the home of many small, unconnected Native American tribes prior to the coming of the Europeans. From east to west the Wappinger steamships included the Paugussetts, Tankiteke, and the Siwanoy. There were also Paquioque and Potatuck inhabitants of Fairfield County. The Dutch explorer Adriaen Block explored coastal Connecticut in the Spring and early Summer of 1614 in the North American built vessel Onrust. The first European settlers of the county, however, were Puritans and Congregationalists from England. Roger Ludlow (1590–1664), one of the founders of the Colony of Connecticut, helped to purchase and charter the towns of Fairfield (1639) and Norwalk (purchased 1640, chartered as a town in 1651). Ludlow is credited as having chosen the name Fairfield. The town of Stratford was settled in 1639 as well by Adam Blakeman (1596–1665). William Beardsley (1605–1661) was also one of the first settlers of Stratford in 1639.

Fairfield County was established by an act of the Connecticut General Court in Hartford along with Hartford County, New Haven County, and New London County; which were the first four Connecticut counties, on May 10, 1666. From transcriptions of the Connecticut Colonial Records for that day:

This Court orders that from the east bounds of Stratford to ye bounds of Rye shalbe for future one County wch shalbe called the County of Fairfield. And it is ordered that the County Court shalbe held at Fairfield on the second Tuesday in March and the first Tuesday of November yearly.

The original Fairfield County consisted of the towns of Rye, Greenwich, Stamford, Norwalk, Fairfield, and Stratford. In 1673, the town of Woodbury was incorporated and added to Fairfield County. In 1683, New York and Connecticut reached a final agreement regarding their common border. This resulted in the cession of the town of Rye to New York. From the late 17th to early 18th centuries, several new towns were incorporated in western Connecticut and added to Fairfield County, namely Danbury (1687), Ridgefield (1709), Newtown (1711), and New Fairfield (1740). In 1751, Litchfield County was constituted, taking over the town of Woodbury. The final boundary adjustment to Fairfield County occurred in 1788 when the town of Brookfield was incorporated from parts of Newtown, Danbury, and New Milford, with Fairfield County gaining territory from Litchfield County.

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