Turkey's biological diversity is considerable because of its biogeographical positions, therefore it is plentiful in terms of diversity in animal genetic resources. Genetic diversity is important in sustainable breeding and conservation programs in livestock. The aim of this study was to determine the genetic structure of Yalova genotype, Kivircik, Tahirova and Es,me sheep breed by using twenty microsatellite markers. A total of 223 Turkish native unrelated sheep (Yalova, Kivircik, Tahirova and Es,me) which were raised in sixteen flocks located in four different provinces (Kirklareli, canakkale, Yalova ve Us,ak) were investigated. A total of 543 alleles were found. The number of loci showed deviations from Hardy-Weinberg equilibrium ranged from 11 (Kivircik) to 17 (Yalova). Although a total of 183 private alleles were detected, only 21 of them had allele frequency above 0.05. The number of observed alleles differed from 42 (for OarFCB20 and ILSTS5) to 20 (for OarCP34 and DRBP1). The highest Ne and PIC values (19.23 and 0.95, respectively) were also observed for ILSTS5 locus. While expected heterozygosity (He) ranged between 0.83-0.95, observed heterozygosity differed from 0.69-0.95. These results can be used for the initiation of registration studies for Yalova after combining phenotypic data evaluations.