Three Egyptian sheep populations, collected from three geographically isolated regions namely Siwa, El-Dakhla and El-Farafra oases of the Egyptian western desert, were investigated using six polymorphic microsatellite markers and electrophoretic protein by SDS-PAGE. Six polymorphic microsatellite markers and electrophoretic protein were used to reveal that the genetic diversity, conduct genetic structure and assignment of microsatellite. The results indicated that; one hundred and five alleles were detected; 34 are common alleles and 71 specific alleles across six loci (67.62%). Thirteen specific alleles for Siwa sheep population ranged from 1 to 5. Also, for Dakhla sheep population 21 alleles ranged from 1 to 8. While 37 ones were obtained in the case of Farafra sheep population ranging from 1 to 14. When the heterozygotsity is high we will have the highest effective number of alleles (ENA) and the expected heterozygosity (gene diversity). The highest ENA was 10.29 for BM1314 when HE was 0.94, while the lowest ENA was 2.22 for BM8125 when HE was 0.58 with El-Dakhla sheep population. The protein profile for 33 sheep population samples collected from three different regions, Siwa had 20 protein bands that MW ranged from 17 to 269KDa. At the same concentration of protein and molecular weight, the band's volume or intensity values changed from sample to other. The homogeneity of individual Siwa samples was 30%. El-Dakhla population had 23 protein bands that ranged from17 to 283KDa. The heterogeneity's El -Dakhla population was 74%. While, El-farfra populations varied in electrophoretic protein pattern, it had 21 bands that ranged from 17 to 252 KDa. The homogeneity percentage was 24%. Finally, protein profile can be used as a marker depending on the presence or absence bands, band intensity, molecular weight and relative front values.