This study evaluates the genetic diversity of silver (Hypophthalmichthys molitrix Val.) and bighead (Hypophthalmichthys nobilis Rich.) carps raised in aquaculture in Belarus using genotyping of 11 microsatellite loci. The results show moderate genetic diversity for silver carps and relatively high diversity for bighead carps. These findings suggest the possibility of grouping individuals for breeding programs, including commercial fish production. However, special attention should be paid to the selection of breeding pairs based on molecular genetic analysis. A scheme for differentiating hybrid individuals between silver and bighead carps using five microsatellite loci was proposed, which can be used as a minimally invasive rapid test in breeding and reproductive programs for these fish species. The study also highlights the importance of genetic diversity in aquaculture, as well as the potential for inbreeding and hybridization between the two species, which could negatively impact breeding programs. The results indicate that bighead carps have higher genetic diversity than silver carps, which is important for maintaining genetic variability and improving breeding efficiency. The study also shows that the genetic diversity of the studied populations is sufficient for breeding purposes, despite the potential for inbreeding. The results suggest that the use of microsatellite loci can be an effective tool for identifying hybrids and managing breeding programs in aquaculture.This study evaluates the genetic diversity of silver (Hypophthalmichthys molitrix Val.) and bighead (Hypophthalmichthys nobilis Rich.) carps raised in aquaculture in Belarus using genotyping of 11 microsatellite loci. The results show moderate genetic diversity for silver carps and relatively high diversity for bighead carps. These findings suggest the possibility of grouping individuals for breeding programs, including commercial fish production. However, special attention should be paid to the selection of breeding pairs based on molecular genetic analysis. A scheme for differentiating hybrid individuals between silver and bighead carps using five microsatellite loci was proposed, which can be used as a minimally invasive rapid test in breeding and reproductive programs for these fish species. The study also highlights the importance of genetic diversity in aquaculture, as well as the potential for inbreeding and hybridization between the two species, which could negatively impact breeding programs. The results indicate that bighead carps have higher genetic diversity than silver carps, which is important for maintaining genetic variability and improving breeding efficiency. The study also shows that the genetic diversity of the studied populations is sufficient for breeding purposes, despite the potential for inbreeding. The results suggest that the use of microsatellite loci can be an effective tool for identifying hybrids and managing breeding programs in aquaculture.