b. = born
bap. = baptised
c. = christened
c/m = marriage contract
d. = died
d. vita patris = died in the father's lifetime
dsp = (decessit sine prole) died without issue
m. = married
Mr Alexander Thomson of Duddingston, was admitted an Advocate and acquired the half of the lands and mill of West Duddingston from Andrew Murray of Arngask and for which he and his wife, Margaret Preston, had a conjunct charter under the Great Seal on 27 October 1598. He also acquired the east-part of those lands and on his own resignation, he had a new charter for the lands of East and West Duddingston, including the town, on 22 November 1600. He d. after then and before May of 1603, and was father of,
- John Thomson of Duddingston, succeeded his father and had service as heir to him in the lands of East and West Duddingston on 17 May 1603. He dsp before 24 Fenruary 1607, when his brother, Thomas, was served heir to him in his estate.
- Sir Thomas Thomson, 1st Baronet, of Duddingston, (see below).
Sir Thomas Thomson, 1st Baronet, of Duddingston, succeeded his elder brother John, to whom he was served heir in the lands of East and West Duddingston on 24 February 1607, and was created a Baronet of Nova Scotia on 20 February 1636, with remainder to his heirs male. He m. Margaret daughter of Sir John Scrimgeour, 1st Viscount Dundee, (c/m 17 September 1627), and d. before March 1666 having had issue;
- Thomas Thomson, bap. at Duddingston, on 9 December 1627 and dsp before March 1666.
- John Thomson, bap. at Duddingston, on 16 March 1631 and dsp before March 1666.
- David Thomson, bap. at Duddingston, on 18 March 1635 and dsp before March 1666.
- Alexander Thomson, bap. at Duddingston, on 17 January 1636 and dsp before March 1666.
- Sir Patrick Thomas, 2nd Baronet, of Duddingston, bap. at Duddingston, on 24 December 1637 and succeeding his father, he was served heir to him in the lands of East and West Duddingston on 23 March 1666, although his lands being heavily encumbered by debt, they were apprised by Thomas, Lord Dunkeld, and Adam Thomson, Saddler, Burgess of Edinburgh, who had a confirmation for them under the Great Seal on 25 January 1667. He died apparently unmarried, and was buried in the Greyfriars, Edinburgh, on 13 February 1674.
- Sir James Thomson, 3rd Baronet, bap. at Duddingston, on 15 July 1641 and succeeded his brother, Sir Patrick, in 1674. He d. without apparent issue in 1691.
- Lewis Thomson, bap. at Duddingston, on 25 June 1644 and is and is named with his brother James and William in a heritable bond dated in 1665.
- William Thomson, who is included with his brothers James and Lewis, in a heritable Bond dated in 1665. He is also named in a Bond of 1681.
- Jean Thomson, bap. at Duddingston, on 27 December 1638.
- Marie Thomson, bap. at Duddingston, on 29 May 1642.
- Margaret Thomson, bap. at Duddingston, on 25 May 1643 and m. Thomas Galloway, Lord Dunkeld.
- Elizabeth Thomson, bap. at Duddingston, on 24 September 1646 and m. Sir John Gibson of Pentland, (he was widow of Jean, daughter of Mr Alexander Hay, fiar of Kennet, whom he had m. in 1633 and by whom he had issue). They had issue.
- Catherine Thomson, bap. at Edinburgh, on 24 September 1648.
 Laing Charters. No. 2449.
 Greyfriars Burial register.
 His parentage has previously been a matter of some confusion with some authors simply presuming that he was a son of the 1st Baronet, however, this is confirmed by a writ of 1682 when he is styled Sir James Thomson, son of Sir Thomas Thomson of Duddingston. See: RD3/54/263.
 Edinburgh Tests.