Nathaniel married Sybil Todd (38250) , daughter of Eleazer Todd (18838) (12 Oct 1707-30 Nov 1771) & Thankful Heaton (53097) (21 Jan 1706/7-12 Dec 1747). Born 23 Jan 1734/5 in New Haven, CT.56 Sybil was baptized in First Congregational Society, New Haven, on 30 Oct 1762.55 Sybil was baptized as an adult. Sybil died in New Haven, CT on 20 Nov 1805.55 Buried in Hamden Plains Cemetery, Highwood.

Nathaniel and Sybil were second cousins in two ways. James Heaton and Mary Street, and Samuel Todd and Mary Bradley, were great grandparents of each.

Children of Nathaniel and Sybil (Todd) Heaton, born and/or baptized at New Haven:
    i. Sarah Heaton, b. 23 Nov 1755, d. 25 Jul 1825 at Hamden, m. at New Haven 15 Sep 1773 Daniel Gilbert (b. 3 Apr 1750 at New Haven, d. 16 Sep 1804 at Hamden);
    ii. Thankful Heaton, b. 4 Feb 1757, d. 9 Mar 1797 at New Haven, m. there 12 Jun 1776 Capt. Daniel Talmadge (b. 23 Dec 1746 at New Haven, d. there 17 May 1831);
    iii. Sybil Heaton, b. 17 Mar 1759, d. 4 Feb 1835 at Hamden, m. 1st at New Haven 19 Dec 1781 Sackett Gilbert (b. 1 Jun 1755 at New Haven, d. there 27 Dec 1787), m. 2nd Timothy Andrews (b. ca. 1764, d. 16 Sep 1830 at Hamden);
    iv. Patience Heaton, b. 21 Jan 1761, d. 11 Nov 1833 at Hamden, m. at New Haven 17 Oct 1781 Joseph Dorman (b. 28 May 1757 at New Haven, d. 19 Apr 1823 at Hamden);
    v. Joseph Heaton, b. 13 Jul 1764, d. ca. 1821 at Hamden, m. at Hamden 25 Sep 1788 Mary Warner (dau. of Benjamin & Sarah (Tuttle) Warner;
    vi. Phebe Heaton, bp. 7 Sep 1766, d. 18 Oct 1766 æ. 3m;
    vii. William Heaton, b. 2 Feb 1768, d. ca. 1802;
    viii. Nathaniel Heaton, bp. 4 Mar 1770, d. 28 Nov 1784 æ. 14 at New Haven; and
    ix. Willis Heaton, bp. 17 Oc t 1774, d. 14 Sep 1838 æ. 64 at Hamden, m. at East Haven 6 Jul 1795 Amelia Potter (b. ca. 1776, d. 16 Jun 1864 æ. 88 at Hamden, dau. of Philemon & Phebe (Mansfield) Potter.55