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¹ Institute of Fisheries of the National Academy of Sciences of Ukraine, 03164, Kyiv-164, Obukhivska St, 135, Ukraine DOI : 10.4194/2459-1831-v5_1_04 Viewed : 2269 - Downloaded : 1137 The genetic structure of rainbow trout farmed in Ukraine were characterized based on microsatellite loci. The selected set of SSR-markers (Simple-sequence repeats-markers) had a high degree of polymorphism that allowed determining the specificity of each local stock (average PIC value = 0.785 ± 0.034). The microsatellite analysis of rainbow trout from the studied stocks showed a high level of genetic diversity (uHe = 0.825 ± 0.030, PIC = 0.785 ± 0.034, I = 1.836 ± 0.127). The level of allelic diversity of the selected loci was high, where the average number of alleles per locus was 7.833, the effective number of alleles per locus was 5.687. The range of amplicon sizes of the studied loci and private alleles for each local group was determined. The cluster analysis showed the presence of three clusters. The range of genetic variability was presented in the graphical interpretation of the principal coordinates analysis (PCoA). Based on unbiased genetic distances, the Kharkiv and Transcarpathian local stocks were found to be the closest, while the Chernivtsi stock was the most distant from them. Keywords : Rainbow Trout (O. mykiss) Microsatellite Loci, Genetic Structure, Polymorphism