John Floyd married Isabella Maria Hazzard (1773–1859) on December 12, 1793 in Beaufort District, South Carolina. They had twelve children, including U.S. Army General Charles Rinaldo Floyd (1797–1845), Confederate General Richard Ferdinand Floyd (1810-1890), and Colonel Henry Hamilton Floyd (1817–1873). Charles Rinaldo Floyd predeceased his parents, as did his brothers John (1802–1830) and Henry (1808–1811) and sister Melinda (1812–1831). His brother Samuel (1814–1878) did not fight for the Confederacy, nor did he ever formally marry, but sold the remains of Bellevue to a former slave, and lived in St. Marys with a mulatto women, with whom he had six children before he was buried in an unmarked grave in a town cemetery.