In this study, 182 male animals from 12 native sheep breeds, as well as Karacabey Merino and Karagul breeds of Anatolia, wild sheep Anatolian Mouflon (Ovis gmelinii anatolka) were used as the study material. Based on SRY and SRYM18 regions on the Y-chromosome, haplotypes of the populations were analyzed using DNA sequence analyses. The SRY region, A-oY1 allele was observed in all of the individuals studied. On the other hand, four different alleles corresponding to four Y-chromosome haplotypes were detected at the SRYM18 microsatellite region. Among native Anatolian breeds (n=143), H6 haplotype (80.41%), H4 haplotype (9.09%), H8 haplotype (8.40%) and H12 haplotype (2.1%) were identified. H6 haplotype was observed in all 16 individuals of Ovis gmelinii anatolica. Pairwise FST values based on haplotype frequencies were calculated for domestic sheep, and the highest F-ST value was observed between Karagul and Kivircik along with Karagul and Ovis gmelinii anatolica with pairwise F(ST )value of 0.43202 (P<0.01). Y chromosome polymorphism of sheep from Turkey were examined comparatively with the accumulated data in the literature. Out of seven haplotypes (H4, H5, H6, H7, H8, H12, H19) observed in Europe and Asia, 4 haplotypes (H4, H6, H8 and H12) were observed in Anatolia. H12 was a private haplotype of Sakiz, H6 seems to be the predominant haplotype of domestic sheep (79.51%) as well as being the only haplotype observed in Ovisgmelini anatolica. H4 haplotype seemed to be associated with fat tailed sheep migrating to Turkey, entering from south east of Turkey, which may be related with the arrival of nomadic Turks.