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The Governorate was established on January 26, 1822 when the territory of Siberia was divided into two governorates general: West Siberian and East Siberian. Yeniseysk Governorate, with the administrative center of Krasnoyarsk, became a part of East Siberian Governorate General. As of its foundation, the governorate included five okrugs: Achinsky, Kansky, Krasnoyarsk, Minusinsky, and Yeniseysk (with Turukhansky Krai).
On April 17, 1914, Uryankhay Krai (conforming roughly to the territory of modern Tuva) was added to Yeniseysk Governorate. This krai existed until August 14, 1921, when it was incorporated as the Tuvan People's Republic independent of Russia. Apart from Mongolia, however, no other country recognized its independence.
On November 14, 1923, parts of the governorate's Minusinsky and Achinsky Uyezds were merged with one volost of Kuznetsky Uyezd of Tomsk Governorate to form new Khakassky Uyezd. On March 19, 1924, Siberian Revolutionary Committee (Sibrevkom) approved the enlargement of the governorate's uyezds (districts).
On June 23, 1924, new Turukhansky Uyezd was formed in the governorate. Its Yuzhnaya Volost was formed on the part of the territory of Antsiferovskaya Volost of Yeniseysky Uyezd. After that, Yeniseysky Uyezd itself was abolished and its remaining territory split between Kansky and Krasnoyarsky Uyezds. At the same time, Daurskaya Volost of Achinsky Uyezd was transferred to Krasnoyarsky Uyezd.
Also in 1924, parts of Znamenskaya and Tashtypskaya Volosts of Minusinsky Uyezd were transferred to Khakassky Uyezd. The former territory became a part of Charkovskaya Enlarged Volost, while the latter was merged into Tashtypskaya Enlarged Volost.
The governorate was abolished on May 25, 1925, when it was included into newly formed Siberian Krai along with the territories of Oyrat Autonomous Oblast and Altai, Novo-Nikolayevsk, Omsk, and Tomsk Governorates. Achinsky, Kansky, Krasnoyarsky, Minusinsky, and Khakassky Uyezds of the governorate were at the same time transformed into okrugs, while Turukhansky Uyezd was renamed Turukhansky Krai and transferred to Krasnoyarsk Okrug.
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- Архивный отдел Новосибирского облисполкома. Государственный архив Новосибирской области. "Административно-территориальное деление Сибири (август 1920 г. - июль 1930 г.), Западной Сибири (июль 1930 г. - сентябрь 1937 г.), Новосибирской области (с сентября 1937 г.) (Справочник)." Западно-Сибирское книжное издательство, Новосибирск, 1966