Parker and his wife, Lydia (Moore) Parker had seven children: Lydia, Anna, John, Isaac, Ruth, Rebecca and Robert. The Parker homestead formerly stood on Spring Street in Lexington. A tablet marks the spot as the birthplace of a grandson, Theodore Parker, a Unitarian minister, transcendentalist and abolitionist who also donated two of Captain Parker's muskets to the state of Massachusetts; one the light fowling-piece which he carried at Quebec and Lexington and one that he captured. They hung in the Senate Chamber of the Massachusetts State House until a 2018 renovation.