RAPD-PCR was performed using ten random primers to identify the genetic diversity among Rahmani, Chios and their crosses. The appearance of bands on gels would reflect the differences between genotypes of the examined animals. The differences would be detected by number and size of present or absent bands with each primer which could be used as positive or negative genetic markers to distinguish between breeds and their crosses. Primers A7, C7 and C1 were used for fingerprinting to identify the Rahmani breed, where they produced bands of 454 and 724 bp, respectively only with Rahmani breed. Presence of band at 410 bp with primer A9 would be used as a genetic marker for Chios breed. The presence of bands 1634, 1105, 223 and 187 bp with primer B17 and also bands 735, 683, 425 and 395 bp with primer A9 could be used as a fingerprinting for cross (½ C ½ R). Presence of bands 173, 132 and 122 bp with primer A5 would be used as a genetic marker for the reciprocal cross (½ R ½ C). The results of molecular DNA of the experimental sheep breeds and their crosses, showed that polymorphism within crosses is higher than polymorphism within the pure breeds of Rahmani and Chios. Fragments generated by primers showed a polymorphism ratio of 10.8 % between Rahmani and Chios and 25 % between crosses (½ C ½ R and ½ R ½ C). Also, the similarity between Rahmani and Chios breeds was 89.1 %, while it was 75 % between crosses. The results asserted that fingerprinting (RAPD-PCR genetic marker) technique would be a useful tool to differentiate sheep breeds and their crosses.