With regard to its historical background, natural conditions and political geography, Caucasus is made up of a variety of races, cultures and followers of different rituals and religions. Historical links of Caucasus residents with Iranian culture and civilization resulted in their adherence to Iranian governments in equilibrium with Roman, Ottoman and Russian policies. Following the collapse of the Safavids, which was simultaneous with Tsarist Russia’s being at the height of its power and a hundred years away from the wars of Iran & Russia, political instability of Iran, continual installation and downfall of several governments, absence of power in the region, insecurity and internal pressures as well as foreign interventions, all and all paved the ground for the separation of Caucasus from Iran. In this period of destabilization and turmoil in the government of Iran, religious heterogeneity of Georgian and Armenian citizens of Iran and efforts of the powerful Christian Tsarist Russia turned out to be one of the underlying factors that laid the groundwork for Christian Caucasians’ separatism from Iran. Although their efforts for separatism did not by any means meant that residents of Caucasus had a desire to join Russia, the course the event took ended in such an annexation. Exploiting the analytical method in historical research the present article aims at exploring the role religious heterogeneity played in the separation process of Caucasus from Iran. Findings demonstrate that next to various political factors, religious heterogeneity had had an important effect on the unexpected course of events.