Following the annexation of Bessarabia by the Russian Empire in 1812 the Russian Orthodox Church established the Eparchy of Chişinău and Khotin under Metropolitan Gavril (Bănulescu-Bodoni) to care for the region's Orthodox Christians.
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Following Moldovan independence from the USSR the Holy Synod of the Russian Orthodox Church granted the Church's eparchies in Moldova autonomy as the Moldovan Orthodox Church, with Archbishop Vladimir (Canterean) of Chişinău becoming first hierarch of the Church of Moldova as Metropolitan of Chişinău and All Moldova.
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The Diocese of Bălți and Fălești was established on October 6, 2006, by the Holy Synod of the Russian Orthodox Church out of the territory of the Diocese of Chişinău.