Analysis of microsatellite loci is highly informative in recon- structing the historical processes underlying the evolution and differ- entiation of animal populations. This study ušed 13 polymorphic mi­crosatellite markers recommended by FAO and ISAG to analýze the genetic diversity, genetic structure, variation, and phylogenetic rela- tionship of 6 Central European sheep breeds (Czech Wallachian, CWA, n – 36, Šumava, S = 46, Slovák Wallachian, SWA, n = 59, Improved Wallachian, IPW, n = 59, Swiniarka, SWI, n = 35, and Uhruska sheep UHR. n = 19). The 172 alleles were observed in 254 animals. The num- ber of observed alleles per locus varied from 7 to 17 per locus (average of 13.23). The mean number of effective alleles per locus was 5.77, with PIC ranging from 0.613-0.907 (equal to 0.77). Fst within subpopula- tions showed a low level of inbreeding. Nei’s genetic distances between breeds were calculated, and results showed that the smallest distance was recorded between CWA and SWA (0.108).