John married Martha Hubbard, daughter of William Hubbard & Judith Knapp. Born ca 1613 in England. Martha died on 13 Jul 1689.

Martha, daughter of William Hubbard of Ipswich, and sister of Rev. William Hubbard, the early New England historian. She married second, Simon Eyre, of Boston.6

Children of John and Martha (Hubbard) Whittingham, born at Ipswich:
    i. John, d. at Boston, 7 Nov 1653;
    ii. Martha, m. Dr. John Clark, of Boston (d. 17 Dec 1690);
    iii. Richard, attended Harvard 1656-1657, d. at England unmarried;
    iv. William, b. ca. 1640, d. bef. 1700 in England while seeking to recover the English estates of his family, m. Mary Lawrence (d. 1671, dau. of John Lawrence of Ipswich and New York City), graduated Harvard 1660, settled in Boston;
    v. Elizabeth; and
    vi. Judith, d. at Boston 27 Mar 1656.6