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John Boden Thomson was born on 14 April 1841 at Kirkpatrick, Kirkcudbrightshire. He studied at Western College and Highgate Missionary College. He married Elizabeth Edwards in 1869. In the same year he was appointed to Matabeleland with the London Missionary Society. He was ordained on June 17 at Trinity Presbyterian Church, Newcastle-upon-Tyne. Thomson and his wife sailed on 9 August 1869, and arrived at Inyati, Matabeleland on 29 April 1870. Thomson was initially posted to the Matabele Mission, where Robert Moffat, William Sykes and Thomas Morgan Thomas were already based. He was to replace Thomas, who was due to return to England. During his service in Matabeleland, Thomson was able to negotiate the grant of a valley 50 miles from Inyati with the Matabele Chief, Lobengula. The site was to form the basis of the new Hope Fountain Mission - a difficult station, which was to be destroyed twice through local conflict before the end of the nineteenth century.
In 1876, Thomson was recalled to England to discuss the possibility of establishing a new Mission at Ujiji on Lake Tanganyika. Together with Roger Price, he was appointed leader of the Central Africa Mission to Ujiji. Leaving his family in England, he sailed for Zanzibar on 6 May 1877. The party, including Thomson, Roger Price, Elbert Sellis Clarke, Edward Coode Hore, Arthur William Dodgshun and Walter Hutley, left Zanzibar for the Ujiji on 21 July 1877. The expedition was beset by difficulties. To travel across Central Africa with ox-drawn wagons proved impracticable, and after deliberation the Mission members decided that their original objective of reaching Ujiji without establishing intermediate stations was over ambitious. Price was dispatched to England to consult with the Directors of the London Missionary Society. The remaining members decided to press on to Ujiji. Clarke withdrew from the Mission in January 1878. When Price failed to return from England, Thomson was appointed overall leader of the expedition (February 1878). The party set out from Kirasa on 29 May 1878. Thomson's group arrived in Ujiji on 23 August 1878. Dodgshun's group failed to reach Ujiji until 27 March 1879, Dodgshun dying seven days after his arrival. Thomson himself died suddenly of a fever on 22 September 1878.