The colony's first settlements were at Little Harbor, Dover, Portsmouth and Exeter. These towns agreed to unite in 1639 and in 1641 agreed to join with Massachusetts Colony. The crown set New Hampshire apart in 1679, reunited it with Massachusetts again in 1688, and separated it out one last time in 1691, at which point it became the royal Province of New Hampshire.

New Hampshire did not get its own colonial governor until 1741.

The disputed New Hampshire Grants territory (New Hampshire claimed it, a judge awarded it to New York) later became the state of Vermont.