On October 27, 1858, Eliot married Ellen Derby Peabody of Salem Massachusetts (1836–1869) in Boston at Kings Chapel. Ellen was the daughter of Ephraim Peabody (1807-1856) and Mary Jane Derby (1807-1892), great-great-granddaughter of Elias Hasket Derby (1739-1799). They had four sons, one of whom, Charles Eliot (November 1, 1859 – March 25, 1897) became an important landscape architect, responsible for Boston's public park system. Another son, Samuel Atkins Eliot II (August 24, 1862 – October 15, 1950) became a Unitarian minister who was the longest-serving president of the American Unitarian Association (1900–1927) and was the first president granted executive authority of that organization.