Turkish Karayaka sheep breed that is one of the important native breed at Black Sea Region in Turkey was genotyped for 13 RAPD primers. Genotypes of 100 were collected from five different herds (BA, BF, LA, LD and KP herds) localized in the Samsun territory. The genetic similarity was obtained on the dendrograms individuals and herd. Within herds, individuals showed a similarity index between 0.857 to 0.420. The similarity index between populations ranged from 0.520 to 0.710. The binary results also were utilised by principal component analysis for comparison of herds and individuals. The genetic relationship of animals shows a difference among herds in terms of number of RAPD bands. These results show that some herds are effected possibly from other sheep breeds or reared purely such as KP.