In 1517, Martin Luther left the Catholic Church and began the Protestant Reformation. This began a period in which new churches, not under the control of the Catholic Church and the Pope, were founded. In England, King Henry VIII declared himself the head of the Church of England. Henry and Elizabeth, who became queen in 1558, did not object to the practices of the Catholic Church and wanted to control the church. There developed a large group of people who wished to reform and change the church. They became known as the "Puritans". They wanted to purify the church and simplify the services and practices. A smaller group became known as "Separates", as they believed in separating themselves from the church.

In 1603, James I became king, and promised to "hurry them out of the land", referring to the Separatists. The Separatists became alarmed and many decided to leave England and move to the Netherlands, a country that has always been open to religious dissidents (people who disagreed with standard beliefs). The Separatists then became pilgrims; people who traveled for religious reasons. The pilgrims were not happy in the Netherlands. It was not home. The people did not speak English, and the fear existed that Catholic Spain would reassert control over the country. They petitioned to establish a colony in the New World. The London Company which had recently received a charter to establish a colony in New England agreed to allow the Separatists to establish a colony at the mouth of the Hudson River.