Summary Forty-eight isolates of hydatid cyst collected from sheep and camels slaughtered in different areas of Iran were analyzed by polymerase chain reaction and restriction fragment length polymorphism techniques. The results indicated that the isolates could be categorized into two distinct and uniform genotype grouping, the camel/dog strain group (Genotype 6) and cosmopolitan common sheep strain group (Genotype 1) of E.granulosus. These isolates can potentially act as a risk factor for human health in the country.