Allen married Ruth Todd (38254) , daughter of Eleazer Todd (18838) (12 Oct 1707-30 Nov 1771) & Thankful Heaton (53097) (21 Jan 1706/7-12 Dec 1747). Born on 14 Sep 1744 in New Haven, CT.56 Ruth was baptized in North Haven, CT, in 1782. She was baptized as an adult.

Children of Allen and Ruth (Todd) Cooper, born at New Haven and baptized at North Haven:
    i. Elisha Cooper, b. 16 Apr 1771, d. young, after 1782;
    ii. Esther Cooper, b. 11 Sep 1777, d. 9 Mar 1867 at Hamden, m. at there 30 Mar 1806 Levi Bradley (b. 19 Aug 1757 at New Haven, d. 15 Mar 1823 at Hamden); and
    iii. Jesse Cooper, b. ca. 1779, d. 12 Nov 1844 at Hamden, m. 5 Jan 1803 Anna Hubbard (b. 15 Jun 1782 at New Haven, d. 10 Apr 1868 at Hamden).6,55