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The article presents data on genetic variability and differentiation of three species of cyprinid fishroach Rutilus rutilus, ide Leuciscus idus and dace Leuciscus leuciscus baikalensis in the rivers of Siberia, Russia. From the three species studied ide has the lowest indices of genetic variability and more pronounced population differentiation. About 40% of isozyme loci are polymorphic in this species and the same percentfor nuclear DNA inter-simple sequence repeat (ISSR) markers; interpopulation component accounts for 62% of genetic variability. In roach indicators of genetic variability are higher, especially for DNA markers (67%), and interpopulation differentiation is less pronounced (FST = 0.550; GST = 0.214). Dace has the most significant genetic diversity and low differentiation of populations. 48% of the isozyme loci and 83% of multilocus DNA markers are polymorphic in this species, the interpopulation component accounts for 27% and 19% for two types of markers, respectively. In comparison with allozymes, ISSR markers provide higher estimates of genetic distances while making intrageneric comparisons and similar or somewhat lower valueswhile making a comparison of different groups. Isozyme markers provide more precise geographical differences of population groups of fish.