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Dispatched on a mission to persuade the Emir of Bukhara to free Russian slaves and sign a treaty of friendship with Britain, he was first arrested by the Emir Nasrullah Khan in 1838. In November 1841 Captain Arthur Conolly arrived in Bukhara with part of his remit to attempt to secure Stoddart's release. He was unsuccessful. Both men were executed on charges of spying for the British Empire on 24 June 1842.
In 1845, the Rev Joseph Wolff, who had undertaken an expedition to discover the two officers' fate and who barely escaped with his life, published an extensive account of his travels in Central Asia which made Conolly and Stoddart household names in Britain for years to come.
- Harries, R.; Cattermole, P.; Mackintosh, P. (1991). A History of Norwich School: King Edward VI's Grammar School at Norwich. Norwich: Friends of Norwich School. p. 205. ISBN 978-0-9518561-1-6.
- Beolens, Bo; Watkins, Michael; Grayson, Michael (2011). The Eponym Dictionary of Reptiles. Baltimore: Johns Hopkins University Press. xiii + 296 pp. ISBN 978-1-4214-0135-5. ("Stoddart", p. 255).
- Peter Hopkirk, The Great Game, Kodansha International, 1992, ISBN 4-7700-1703-0, p. 565
The timeline of the Great Game is available online.
- Tom Bissell, Chasing the Sea, Vintage, 2004, ISBN 978-0375727542, pp 247–253
- Stephen M. Bland Does it yurt? Travels in Central Asia or How I Came to Love the Stans, Hertfordshire Press, 2016, ISBN 978-1910886298
- Joseph Wolff, Narrative of a mission to Bokhara, in the years 1843–1845, to ascertain the fate of Colonel Stoddart and Captain Conolly. London: J. W. Parker, 1845. First and second (revised) edition both came out in 1845.
- New York: Harper & Bros., 1845
- Edinburgh and London: William Blackwood & Sons, 1848
- New York: Arno Press, 1970 ISBN 0-405-03072-X
- Elibron Classics, 2001, ISBN 1-4021-6116-6)
- A mission to Bokhara. Edited and abridged with an introduction by Guy Wint. London: Routledge & Kegan Paul, 1969. ISBN 0-7100-6456-X