Abstract In the present study, Echinoccocus granulosus isolates collected from human, sheep and camel samples in Iran were characterized based on rostellar hook morphology of protoscoleces as well as PCR-RFLP. Morphological study on human and animal isolates showed the presence of two distinct strains of the parasite, one in sheep and the other one in camels. In this regard, rostellar hook of sheep isolates were significantly different from those of camel origin, meanwhile human isolates were found to be similar to those isolated from sheep. Molecular analysis of the ITS1 region of rDNA derived from human, sheep and camel isolates were in agreement with the morphological findings. Based on the PCR-RFLP method, the sheep and human isolates appeared to pertain to the same genotype and the camel isolates were appeared to pertain to a different genotype.