Less than four centuries ago the area which is now New Haven was the home of a small tribe of Native Americans, the Quinnipiack, who built their villages around the harbor. They harvested seafood, hunted with bow and arrow for food and furs and grew maize, the staple of their diet.

On April 24, 1638, a company of five-hundred English Puritans led by the Reverend John Davenport and Theophilus Eaton, a wealthy London merchant, sailed into the harbor. They soon discovered that the Quinnipiacks and other local tribes were much distressed by raiding bands of Pequots and Mohawks from surrounding areas. It was for this reason that Momauguin, the sachem of the Quinnipiacks, and other tribe members agreed to sell the tribe's land to the Puritans. In return, the settlers pledged to protect the natives and to allow them the use of the lands on the east side of the harbor.

New Haven's founders not only hoped to create a Christian utopia, they also saw in New Haven's spacious harbor an opportunity to establish a commercial empire that would control Long Island Sound and possibly the coastline as far south as Delaware Bay.

By 1640 a complete government had been established and the settlement, originally called Quinnipiac, was renamed Newhaven. The town plan was based on a grid of nine squares. In accordance with old English custom, the central square, now the Green, was designated a public common. By 1641 New Haven had grown into a community of approximately 800.

Over the next few years, however, the flow of newcomers began to weaken and trade with the outside world shifted more and more to Boston. In an attempt to establish direct trade with England, the settlers managed to assemble enough produce to fill a vessel which would become known as the "Great Shippe." However, after setting sail in January, 1646, the ship and its crew were never heard from again. This disaster ended the dream of creating an economic empire and over the years New Haven became overshadowed by New Amsterdam and Boston.

In 1649, King Charles I of England was accused of treason and beheaded. His son, Charles II, became king eleven years later and sought vengeance against the men who had signed his father's death warrant. Two of them, Colonel Edward Whalley and his son-in-law Colonel William Goffe fled to America and, in 1661, they were hidden by John Davenport in a cave on the top of New Haven's West Rock. They were later joined by a third regicide, John Dixwell. Three of New Haven's streets are named after the regicides and their story has become an integral part of New Haven's history.

In 1664, the forces of King Charles' brother, the Duke of York, seized New Amsterdam. Rather than face the possibility of rule by the Catholic duke, New Haven surrendered its hope of remaining independent and united with the Connecticut Colony. By 1701, New Haven had grown to be the village center of a mainly agricultural township and became co-capital of Connecticut, along with Hartford. It was not until 1873 that New Haven lost its status as co-capital.

In 1700, a small Puritan college known as the Collegiate School was founded in Old Saybrook. Eighteen years later it moved to New Haven, and, after receiving a large benefaction from Elihu Yale, was renamed Yale College. It would eventually become a world renowned university and a major economic factor in the city.