Анотация: The application of gene specific molecular markers in genotyping and genetic identification is of essential significance for preserving genetic diversity. The aim of study was to reveal the genotype profile of two native for Bulgaria cattle breeds - Shorthorn Rhodopean cattle breed (SRc) and Bulgarian Grey cattle breed (BGc). These breeds were genotyped with respect to alfaS1-casein gene (CSN1S1) and kappa casein gene (CSN3) polymorphism by PCR-RFLP assay. The results showed high frequency of the homozygous BB genotype and B allele (70%) of CSN1S1 in SRc breed. Analysis of CSN3 polymorphism revealed that the heterozygous AB genotype was presented with the highest frequency and prevalence of the B allele (54%). Analysis of polymorphism of the CSN1S1 gene in the BGc breed displayed high frequency of the heterozygous BC genotype and B gene allele (57%). The results for CSN3 locus showed superiority of the heterozygous AB genotype and prevalence of the uncommon B allele (51%). Genetic profiles of the Bulgarian local breeds were compared to other European cattle populations to establish the position of the breeds with regard to cattle diversity. It may be concluded that SRc and BGc breeds are with specific genotype profiles similar to other cattle population in South-Eastern Europe