In 1637 he joined a venture led by Theophilus Eaton, an indirect relation through his wife, and John Davenport which led to the establishment of a settlement at the mouth of the Quinnipiac River and the founding of the New Haven Colony. Two months later he was sent north to recently founded Hartford on the Connecticut River to negotiate additional land purchases for the New Haven colonists, but decided to instead stay in Hartford, becoming one of the early settlers of the Connecticut Colony. In the colony's first election in 1639 he became one of several Assistants to the General Court. Then, in 1640 Hopkins was elected governor. Because the colony's charter forbade reelection to the governorship, Hopkins and John Haynes (Connecticut's first governor) traded off as governor (save one term by George Wyllys) between 1639 and 1655, each serving as Deputy Governor to the other when not governor.