The present study was conducted to assess the genetic diversity and population genetic structure of three sheep populations namely; Sawakni (SW), Berberi (BR) and Najdi (NJ), in Saudi Arabia, utilizing 45, 18 and 31 individual blood DNA extractions, respectively. Seventeen microsatellite markers were used to genotype these 94 sheep individuals. There were 195 alleles generated employing the 17 microsatellites loci with a mean of 11.47 alleles per locus, with a range of observed and expected heterozygosity from 0.651 to 0.989 and 0.590 to 0.816, respectively.