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In 1261 the Nicaean emperor Michael Palaeologus recaptured Constantinople from the Latins, and an Orthodox patriarch again occupied the see in Hagia Sophia. From 1261 to 1453 the Palaeologan dynasty presided over an empire that was embattled from every side, torn apart by civil wars, and gradually shrinking to the very limits of the imperial city itself. The church, meanwhile, kept much of its former prestige, exercising jurisdiction over a much greater territory, which included Russia as well as the distant Caucasus, parts of the Balkans, and the vast regions occupied by the Turks. Several patriarchs of this late period—e.g., Arsenius Autorianus (patriarch 1255-59, 1261-65), Athanasius I (patriarch 1289-93, 1303-10), John Calecas (patriarch 1334-47), and Philotheus Coccinus (patriarch 1353-54, 1364-76)—showed great independence from the imperial power, though remaining faithful to the ideal of the Byzantine oikoumene.
Without the military backing of a strong empire, the patriarchate of Constantinople was, of course, unable to assert its jurisdiction over the churches of Bulgaria and Serbia, which had gained independence during the days of the Latin occupation. In 1346 the Serbian Church even proclaimed itself a patriarchate; a short-lived protest by Constantinople ended with recognition in 1375. In Russia, Byzantine ecclesiastical diplomacy was involved in a violent civil strife; a fierce competition arose between the grand princes of Moscow and Lithuania, who both aspired to become leaders of a Russian state liberated from the Mongol yoke. The "metropolitan of Kiev and all Russia" was by now residing in Moscow, and often, as in the case of the metropolitan Alexis (1354-78), played a directing role in the Muscovite government. The ecclesiastical support of Moscow by the church was decisive in the final victory of the Muscovites and had a pronounced impact on later Russian history. The dissatisfied western Russian principalities (which would later constitute the Ukraine) could only obtain—with the strong support of their Polish and Lithuanian overlords—the temporary appointment of separate metropolitans in Galicia and Belorussia. Eventually, late in the 14th century, the metropolitan residing in Moscow again centralized ecclesiastical power in Russia.