Sixteen isolates of Echinococcus granulosus, collected from Iranian patients at surgery, and from domestic animals, including sheep, goats, cattle, and camels at slaughterhouses in Tehran and central and southern Iran were analyzed for DNA nucleotide and predicted amino acid sequence variation within regions of the mitochondrial cytochrome c oxidase I (COI) and NADH dehydrogenase subunit I (NDI) genes. A polymerase chain reaction-restriction fragment length polymorphism method, based on the DNA sequence variation in the NDI gene, was also used to rapidly survey the E. granulosus isolates. The isolates were categorized into two distinct and uniform genotype groupings. The analysis clearly indicated that the camel/dog strain (G6 genotype) of E. granulosus as well as the cosmopolitan, common sheep strain (G1 genotype) occur in Iran. The G1 genotype was found present in all four human isolates examined and it was more prevalent in domestic animals than the camel-restricted G6 genotype. In E. granulosus-endemic areas of Iran it is evident, therefore, that the majority of E. granulosus-infected livestock animals can potentially act as reservoirs of human infection, and this has important implications for hydatid control and public health.