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Cystic hydatid disease (CHD) is one of the most important zoonotic diseases in different parts of Iran. While it causes major health problem, there is limited information about its transmission cycles and reservoirs of human infection. Therefore we aimed to characterize the existence Echinococcus granulosus cysts in humans and animals in the province of Isfahan, central region of Iran. We collected hydatid cysts from the liver and lungs of patients who underwent surgery procedure and also cysts were obtained from domestic animals at slaughterhouses. DNA was extracted from the protoscoleces and examined by polymerase chain reaction (PCR) of rDNA internal transcribed spacer1 (ITS1-PCR) and PCR-restriction fragment length polymorphism (PCR-RFLP). In addition, fragments of the genes coding for mitochondrial cytochrome c oxidase subunit 1 (CO1) and NADH dehydrogenase 1 (ND1) were sequenced. Among the two different identified strains/genotypes (sheep and camel), the sheep strain was shown to be the most common genotype of E. granulosus affecting humans, sheep, cattle, goats and occasionally camels. Nine out of 26 camel samples were infected with sheep strain. However the camel genotype was observed in humans, camels and cattle. Seventeen out of 26 camel isolates, 6 out of 31 human and 5 out of 14 cattle samples were infected with the camel genotype. The camel genotypes had PCR and RFLP patterns which were different from the PCR and RFLP patterns of the rest of isolates (sheep strain). The results of this study showed that the 'camel' strain was actual source of infection to humans which circulates between intermediate hosts including camels and cattle, and it confirms the camel-dog transmission cycle in Isfahan., (Copyright © 2010 Elsevier B.V. All rights reserved.)