Sometime in the 1840s Riker married his first cousin Anna E. Elder. Anna was the eldest daughter of Hannah E. Riker, who was the younger sister of his father, James. About 1848 Anna gave birth to Riker's first child, Anna E. Riker. A year or two later she gave birth to a son, John L. Riker Jr. In 1851 Riker's wife, Anna, died of "hysteria". The following year his father James Riker Sr. died and in 1854 his young son, John L. Riker Jr. died of congestion on the brain.
