Although frequently referred to as Captain Allen, Thomas Allen never attained that rank. He retired from the Navy as a Lieutenant in 1798 and his subsequent history and movements and the extent to which he approved of his sons’ later claims, are all far from clear. He had married Catherine Matilda Manning, a daughter of the Rev. Owen Manning the historian of Surrey, at Godalming in 1792. They had three children: (1) John Carter Allen, born at Oystermouth, Glamorgan, 4 August 1795 and baptised there, 5 October 1795; (2) Matilda Allen, born at Oystermouth, Glamorgan, 18 October 1799 and baptised there, 12 January 1800; and (3) Charles Manning Allen, born at Rotherfield Grays, Oxfordshire, 4 July 1802 and baptised there, 3 August 1802. Under their marriage settlement the couple and their future children had a life interest and income from properties in Mare Street and Well Street, Hackney.