Hunter married Lynne Layh in 1973. Hunter's son, Duncan Duane Hunter (born 1976), a major in the United States Marine Corps Reserve, was deployed to Iraq in 2003 and 2004 and Afghanistan in 2007. On November 4, 2008, Duncan D. Hunter was elected to succeed his father as the congressional representative of the California's 52nd congressional district. On August 21, 2018, Duncan D. Hunter and his wife Margaret, were indicted for criminal activity. On March 17, 2020, his son, Duncan Hunter was sentenced by the U.S. District Court Southern District of California to 11 months in prison. In June 2019, federal prosecutors showed that from 2009 to 2016, Hunter had spent campaign funds on extramarital affairs with five women, including lobbyists and congressional staff. In December 2019, Hunter changed his plea to guilty on one count of misusing campaign funds. Hunter has another son, Samuel.