A total of twenty-three Echinococcus granulosus hydatid cysts were collected from infected sheep slaughtered in Nablus abattoir, Nablus – Palestine. Protoscoleces or germinal membranes were used for DNA extraction followed by PCR amplification. Amplified products were analyzed the presence of a fragment of 444 bp of the mitochondrial cytochrome c oxidase subunit 1 (cox1) gene followed by nucleotide sequencing. Overall, 21 hydatid cysts were positive compared to a negative control. The partial sequences of cox1 gene of E. granulosus strains indicated that the sheep in Palestine were infected with genotype 1 (G1), genotype 2 (G2) and genotype 3 (G3). The prevalence of these genotypes was (14/21) 66.7%, (4/21) 19.0% and (3/21) 14.3% for G1, G2 and G3, respectively. Our results showed that twelve strains of G1 belonged to the common haplotype EG01 which is the major haplotype in all the geographic populations. Phylogenetic analysis also showed that two sequences of G1 genotype which have GenBank accession No. KC109657 and KC109659 were corresponding to G1.4 micro-variants. Only the sequence of GenBank accession No. KC109652 identified in our study as G2 was found to have complete identity to the original sequence described for the cox1 gene (GenBank accession No. M84662). It is concluded that G1 genotype is the predominant genotype in sheep in Palestine. Therefore, these findings should be taken into consideration in developing prevention strategies and control programs for hydatidosis in Palestine.