This study was undertaken to determine the genetic structure and the diversity among 2 local cattle breeds from Bulgaria, the Rhodope Shorthorn and Grey cattle. A panel of 11 microsatellites was used for the evaluation. For these loci, allele frequencies, heterozygosity, HWE, genetic disequilibrium, genic differentiation were determined. Both populations displayed a relatively high level of genetic variation as estimated by allelic diversity and heterozygosity. Heterozygosities ranged from 0.5424 /SPS 115/ to 0.8983 /TGLA 227/ for the Rhodope population and 0.6333 /TGLA 53/ to 0.9333 /TGLA227/ for Grey cattle, with similar average values for the two groups - 0.7858 and 0.7757. These results clearly suggest that these breeds are suitable to preserve as a genetic resources.