Four Saudi Arabian indigenous sheep populations including Najdi, Hbsi, Arb, and Naemi were genotyped for 16 microsatellite markers recommended by the food and agriculture organization (FAO). This study aims to provide information on the genetic structure of the breeds analyzed and give indications and proposals for the cross breeding program. All loci were polymorphic in all populations and locus combinations were at Hardy-Weinberg equilibrium except ILSTS044, ILSTS005, MAF209, HUJ616, OARFCB226 and SRCRSP09 (P<0.05). There was substantial genetic variability within sheep populations, with average heterozygosity range of 0.759-0.811 based on expected hetrozygosity. It was observed that the four sheep populations showing the lowest level of inbreeding on the basis of heterozygote deficiency. The lowest genetic distance (0.013) was obtained between Hbsi and Najdi and the highest genetic distance (0.146) between Arb and Hbsi. Estimates of inbreeding coefficient (FIS) were significant for three breeds, except for Arb breeds (P<0.05). The sequence results of the 16 microsatellite markers were sequenced and then phylogenetic tree based on unbiased distances was drawn using MEGA 4. To study the genetic relationships among sheep populations, a principal coordinate analysis (PCA) based on Nei standard distances was performed which indicated a conservation program is needed in these sheep population since most of them are in danger of inbreeding. پرونده مقاله