On 13 Oct 1726 when Nathaniel was 22, he first married Phebe Cooper (21394) , daughter of Ens. Joseph Cooper (11 Sep 1683-1747) & Abigail Smith (7960) (11 Oct 1683-aft 1747), in New Haven, CT.56 Born on 8 Jun 1707 in New Haven, CT.56 Phebe died in New Haven, CT, on 10 Apr 1750; she was 42.55 Buried in City Burial Ground, New Haven.

Nathaniel second married Thankful Bassett (10412) , daughter of Samuel Bassett (3464) (15 Feb 1654-8 Apr 1716) & Mary Dickerman (3474) (1 May 1659-28 Nov 1728). Born on 11 Oct 1702 in New Haven, CT.56 Thankful died in New Haven, CT, on 1 Jan 1787; she was 84.55 Buried in City Burial Ground, New Haven.

Children of Nathaniel and Thankful (Bassett) Yale, born at New Haven:
    i. Mary Yale, b.12 Dec 1729;
    ii. James Yale, b. 21 Jul 1731, d. 23 Sep 1731;
    iii. Nathaniel Yale, b. 29 Aug 1732, d. young;
    iv. Ruth Yale, b. 19 May 1735;
    v. Thankful Yale, twin, b. 19 May 1735;
    vi. Rebecca Yale, b. 9 Oct 1737, m. Moses Potter; and
    vii. Nathaniel Yale, b. 16 Sep 1740.

On 29 Oct 1730 James married Hannah Peck (24675) , daughter of James Peck (17 Feb 1679-1760) & Abigail Morris (9566) (22 Aug 1683-bef 1729), in New Haven, CT.56 Born on 10 Aug 1710 in New Haven, CT.56 Hannah died on 8 Apr 1777; she was 66.