Triaenophorus crassus is the causative agent of muscular trienophorosis in fish, especially pathogenic for juvenile salmonids and coregonids. The purpose of this work was to analyze the infection of coregonids with T. crassus plerocercoids in the Chivyrkuisky Bay of the Lake Baikal and Tsipo-Tsipikanskiye (Bauntovskie) lakes (basin of the Lena River, Transbaikalia). Level of infection with plerocercoids T. crassus in coregonids from 1976 to 2013 in the Chivyrkuisky Bay of the Lake Baikal did not cause concern: the prevalence in the Baikal omul did not exceed 23.6%; intensity was no more than 6 specimens; the prevalence in the Baikal whitefish is up to 5.0%. At the same time, in 1954, in the Chivyrkuisky Bay, a higher level of infection of the Baikal omul was noted (the prevalence was 44.4%; the intensity was 1–9 specimens), which does not allow us to exclude a recurrence of this situation in the future. There was a sharply different situation in terms of infection of coregonids with T. crassus plerocercoids in two lakes of the Tsipo-Tsipikanskaya group: in the lake Bolshoye Kapilyushi, the prevalence of this cestoda is ten times higher than in the lake Baunt. It is likely that such contrasting levels of infection were associated with the difference in the location of the habitats of pike (the definitive host of T. crassus) and coregonids in these lakes: the coincidence in the lake Bolshoye Kapylyushi and divergence in the lake Baunt.