Abstract <p>The results from comparative analysis of morphometric and molecular genetic methods for interspecific, intraspecific, and interline differentiation of silver andbighead carps from the broodstocks of Krasnodar krai and Rostov oblast are presented. Using discriminant analysis of morphometric feature indices, four silver carp lines and two bighead carp lines were differentiated. The use of indices with the highest contribution to discriminant functions for practical application in selective breeding programs is discussed. The possibility of using morphotype analysis to identify interline and interspecific hybrids is also assessed. Molecular genetic analysis was conducted using 11 polymorphic microsatellite loci. The results from principal component analysis of genetic distances and cluster analysis showed that all studied samples fell into four clusters. One cluster included individuals of local bighead carp lines from Krasnodar krai and Rostov oblast, and the other cluster included larvae of hybrid origin. The silver carp cluster was found to be divided into two subclusters, which corresponded to two lines within the species.</p>