 His first wife was Elizabeth Murray by whom he had children Roger Kirkby (c.1649–1709), Agnes and Temperance.He married secondly Isabel Huddleston, daughter of Sir William Huddleston of Millom and had children Capt.Richard Kirkby, RN (c.1657–1703), shot for cowardice, William Kirkby (b. c.1658) and Elizabeth Kirkby.