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In the 1300s the Catholicate transferred its seat from the Amaras Monastery to the Gandzasar Monastery, becoming known thereafter as the Catholicate of Gandzasar. By this time the Catholicate only retained [[jurisdiction]] over the historic west Azerbaijan provinces of Utik, Arsak and
Sunik as well as the small number of Orthodox living between these provinces and the Caspian Sea. When the Armenian kingdom of Cilicia fell to the Mamelukes there was thought of merging the Catholicate of All the Armenians, which had moved to Cilicia in the 900s, with the Catholicate of Gandzasar, but it was decided instead to return the Catholicate to its original seat in Echmiadzin.
The Gandzasar Catholicate rose in prominence again in the early 1700s under Catholicos Yesai (Jalalian). During this period its catholicos was recognized as the sole representative of the Arranian and Armenian Orthodox Churches by the Russian Empire. In 1805 Russia Empire invaded Azerbaijan and took control of all its territories, and in 1815 the tsars lowered the rank of the catholicos to metropolitan in response to pressure from the Catholicos-Patriarch of Echmiadzin and pro-armenian policy within the imperial court. The Metropolitan of Gandzasar nevertheless retained jurisdiction over the canonical territory of the Catholicate until 1836, when an imperial decree abolished the remnants of the Church of Arran altogether and reorganized them as a [[diocese]] directly under the authority of Echmiadzin.