Specific karyotype structure and chromosomal polymorphism was investigated in the populations of Sergentia nebulosa Linevitsh et al., 1984 and Sergentia assimilis Proviz V. et Proviz L., 1999, the deep-water endemic chironomid species (Diptera, Chironomidae) from the Baikal Lake. The distinguishing feature of the karyotypes of these species, compared to the other Baikalian Sergentia, is well-developed nucleolus in region 6 of arm C. Both species display the presence of interspecific population polymorphism, determined by the structure of this arm. In some populations, chromosome regions from 4 to 6 contain a homozygous inversion, which is absent in the other populations. The distinguishing karyotype feature of S. assimilis, which shares fluctuating homozygous inversions with the other species, is the presence of two species-specific homozygous inversions. These are the secondary overlapping inversion in arm A, regions 2 to 7, and the inversion in regions 4 to 10 of arm G. Both species of interest contain nucleolus organizer in region 10 of arm G. In populations of S. nebulosa, six heterozygous inversions localized in arms A, B, C, F, and G were discovered. The highest number of heterozygotes for inversions (71%) was observed in the population from Southern Baikal. In arm B of S. assimilis, one heterozygous inversion and heterozygosity for nucleolus organizer in the chromosome region 16 was detected. Chromosomal evolution of Baikalian Sergentia, and the role of inversion polymorphism in the population adaptation is discussed.