Purpose. The goal of this work was the selection of microsatellite markers to study the genetic structure of populations of silver (Hypophthalmichthys molitrix) and bighead (Hypophthalmichthys nobilis) carps of fish farm JSC "Donrybkombinat" of Donetsk region. Methodology. Products of amplification were separated in 2 % agarose gel in 1×TBE buffer. Visualization was performed with help of transilluminator in UV-region of the spectrum and photographing of electrophoregrams by digital camera. Processing and analysis of gels were performed using program TotalLab v2.01. The frequency of each amplicon by particular locus was determined as a percentage from the total number of amplicons at this locus. Statistical analysis of results was carried out using programs Excel, «Biosys-1». Findings. At the results of investigations of populations silver carp and bighead carp were analyzed genotypes of individuals by using three microsatellite DNA loci: MFW 15, MFW 23, MFW 06. Originality. It has been first shown that to investigate genetic structure of Ukrainian silver and bighead carps of JSC "Donrybkombinat" the most informative microsatellite loci were MFW 15 and MFW 23. Practical value. Microsatellite loci MFW 15 and MFW 23 used in research were suitable for interspecies differentiation of Ukrainian silver and bighead carps and can be applied in population-genetic investigations of fishes.