Marriages and issue
Throckmorton married first Muriel Berkeley (died 1542), the daughter of Thomas Berkeley, 5th Baron Berkeley (1472–1532), by his first wife, Eleanor Constable (c. 1485–1527), daughter of Sir Marmaduke Constable (c. 1456–1518), by whom he had a son and four daughters:
Thomas Throckmorton of Coughton (1534 – 13 March 1615), who married, about 1556, Mary Whorwood (c. 1535 – 28 April 1607), by whom he had two sons, including John Throckmorton (1580–1614/15), esquire, father of Robert Throckmorton, 1st Baronet (1599–1650), and five daughters.
Elizabeth Throckmorton (born c. 1535), who married Sir John Goodwin (died 1596/97) of Winchendon, Buckinghamshire.
Katherine Throckmorton (c. 1532 – 12 February 1580), who married firstly Henry Norwood (c. 1523 – 1556) of Leckhampton, Gloucestershire, son of Ralph Norwood (died 1560/61) and Jane Knight, by whom she had issue including William Norwood (1548–1632), who married Elizabeth Lygon; she married secondly John Williams.
Mary Throckmorton (died 1603), who married Edward Arden of Park Hall, executed at Smithfield 20 December 1583, by whom she had a son, Robert Arden, and two daughters: Margaret Arden, who married John Somerville, and Catherine Arden, who married Sir Edward Devereux, 1st Baronet of Castle Bromwich, son of Walter Devereux, 1st Viscount Hereford.
Anne Throckmorton (1540–1603), who in 1557 married Ralph Sheldon (c. 1537–1613) of Beoley.
Throckmorton married, secondly in about 1542, Elizabeth Hussey (c. 1510 – 23 January 1554), widow of Walter Hungerford, 1st Baron Hungerford of Heytesbury (died 1540), by whom she had been notoriously ill-treated, and daughter of John Hussey, 1st Baron Hussey of Sleaford (1465–1537) by his second wife, Lady Anne Grey (c. 1490 – after 1537). By his second wife Throckmorton had four daughters:
Muriel Throckmorton (died 1615), who married Sir Thomas Tresham (1543–1605) of Rushton Hall, Northamptonshire, by whom she was the mother of the conspirator, Francis Tresham.
Anne Throckmorton (died after 1605), who married Sir William Catesby (1547–1598) of Lapworth, Warwickshire, on 9 June 1566 at Ashby St. Ledgers, Northamptonshire, and had children, including Robert Catesby.
Elizabeth Throckmorton, who married Sir Anthony Tyringham of Tyringham, Buckinghamshire, by whom she had a daughter, Elizabeth Tyringham, who married Sir Robert Fisher, the first of the Fisher baronets.
Temperance Throckmorton, who married Sir Randal Brereton (died 1611), by whom she had no issue.