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Just before the second Soviet occupation in 1944 and the dissolution of the Estonian synod, the [[primate]] of the church, Metropolitan Aleksander, went into exile along with 21 clergymen and about 8,000 Orthodox believers. The Orthodox Church of Estonia in Exile with its synod in Sweden continued its activity according to the canonical statutes, until the restoration of Estonian independence in 1991. Before he died in 1953, Metr. Aleksandr established his community as an [[exarchate]] under Constantinople. Most of the other bishops and clergy who remained behind were deported to Siberia. In 1958, a new synod was established in exile, and the church organized from Sweden.
[[Image:Ecum. Patriarch Bartholomew.jpg|thumb|125px|left|Patr. [[Bartholomew I (Archontonis) of Constantinople|Bartholomew I of Constantinople]]]]
Following the breakup of the Soviet Union, divisions within the Orthodox community in Estonia arose between those who wished to remain under Russian authority and those who wished to return to the jurisdiction of the Ecumenical Patriarchate, with the dispute often taking place along ethnic lines, many Russians having immigrated to Estonia during the Soviet occupation. Lengthy negotiations between the two patriarchates failed to produce any agreement.
In 1999, the church gained a resident hierarch (it had been under the Archbishop of [[Church of Finland|Finland]] as ''[[locum tenens]]''), Metropolitan [[Stephanos (Charalambides) of Tallinn|Stephanos (Charalambides)]], who had formerly been an [[auxiliary bishop]] under the Ecumenical Patriarchate's Metropolitan of France.