Mitochondrial genes have more power than nuclear genes in reconstructing phylogenetic relationships among closely related species because of their faster sequence evolution. The aim of this study was to use the complete or near-complete sequences from three mitochondrial genes (cox1, nad1 and atp6) and partial sequences of the 12S rRNA gene to infer relationships among isolates of Echinococcus granulosus from Iran. Two hundred and twenty-nine isolates of E. granulosus were collected from cattle, camels, sheep, buffalo and goats from different geographical areas. Most individuals were found to possess the G1 genotype but some of the camel samples belonged to the G6 genotype. Newly designed primers for cox1, nad1 and atp6 genes amplified bands of 1830, 708 and 1157 bp for the G1 genotype and 1856, 705, 1054 bp for the G6 genotype, respectively. The result of this survey showed that atp6 and nad1 genes are good molecular markers for identifying E. granulosus isolates from a range of hosts in Iran.