The fauna of ciliates - endobionts of the rumen of wild reindeer from Yakutia was investigated. In total, 23 species of ciliates belonging to 10 genera from the families Ophryoscolecidae and Isotrichidae were found. Among them, seven species of ciliates specific to reindeer have been identified. The comparative analysis of the species diversity of endobiotic ciliates in reindeers from different geographical regions was carried out. Based on molecular phylogenetic analysis using SSU and ITS-1 sequences, the question of the species status of Epidinium gigas, ciliates specific to reindeer, was discussed.