Born in Dublin, she was the daughter of Dr William Stokes and his wife Mary (née Black). One brother, Whitley Stokes, was a leading Celticist, a second, Sir William, followed their father into medicine and was a leading surgeon. Important figures in the field of antiquities such as artist Sir George Petrie, lawyer and poet Sir Samuel Ferguson, Edwin Wyndham-Quin, 3rd Earl of Dunraven and Mount-Earl, and historians James Henthorn Todd and William Reeves were frequent visitors to the Stokes family home, and this is said to have begun Margaret's interest in Irish antiquities.
Her first published works were illustrations and illuminations for an 1861 edition of Ferguson's poem The Cromlech at Howth; the title page conflated parts of the illuminations on two pages of the Book of Kells. In the 1870s she edited Dunraven's Notes on Irish Architecture (3 volumes, 1875–1877) after the author's death in 1871. Her Early Christian Art In Ireland (1887, 2nd edition 1911) was well regarded, and if reviewer Oscar Wilde was unmoved by Stokes' prose, he praised her illustrations. She produced two works on early medieval Irish saints in Europe, Six Months in the Apennines (1892) and Three Months in The Forest of France (1895). Her High Crosses of Ireland was incomplete at her death.
- Caesar Litton Falkiner (1901), Sidney Lee, ed., "Margaret McNair Stokes", Dictionary of National Biography, London: Oxford University Press, III of the Supplement, pp. 362–3
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