The paper presents data on the polymorphism of the interior simple sequence repeats of DNA in the silver crucian carp Carassius auratus gibelio from waterbodies in the Western Siberia. The proportion of the polymorphic ISSR-PCR bands in the silver crucian carp populations from different lakes varied from 40 to 70%, the rate of Nei’s gene diversity being 0.16 – 0.25. Genetic diversity indicators were lower in the populations primarily presented by females, as compared with bisexual ones.