Daniel Perrin was married to Maria Thorel, of Rouen, France, on February 18, 1666. They had five sons and one daughter; Peter, b. 1667, Henry, b. 1669, James, b. 1670, Daniel, b. 1672, William, b. 1673, and Francyntje, b. 1675. He also had three daughters from a second marriage to a woman named Elizabeth. The daughters names are Sara, Elizabet, and Mary. Perrin died on Staten Island after September 6, 1719.
The Staten Island neighborhood of Huguenot is named after him and the other Huguenots who settled in the area during the late 17th century and early 18th centuries.