"The paradox of taxa sizes" is the situation with unclear causes of differences in species number at organisms from the same ecosystem. It occurs frequently among Lake Baikal fauna. A typical example are highest crustacea from orders of Amphipoda (more than 300 species) and Isopoda (6 species). Our results of mathematic computer modelling of the karyotypic evolution suggest that the paradox of taxa sizes can be due to different ranges of chromosomal reorganizations which accompanied the evolution of these groups. The ranges of genomic modifications, in turn, are determined by structural peculiarities of the chromosomes, namely by saturation with heterochromatine. Thus, it is possible that "the paradox of taxa sizes", like "the DNA C-value paradox", is due to the phenomenon of redundant («silent») DNA.