BACKGROUND: Cystic echinococosis (CE) is known to be one of the most important zoonotic diseases in different parts of Iran. Even though it causes major health problems, there is limited information regarding its transmission cycles and strain of this infection in eastern Iran. OBJECTIVES: The present study aimed to characterize the strain of Echinococcus granulosus cysts in the slaughtered sheep and goats in Birjand area using morphological and molecular criteria. METHODS: Isolates of E. granulosus were collected from sheep (30) and goats (30) from Birjand slaughterhouse and characterized employing both DNA (PCR-RFLP of ITS1) and morphological criteria (metacestode rostellar hook dimensions). In addition, the fragments of the genes coding for ITS-1 were sequenced. RESULTS: Among the two different identified strains/genotypes (sheep and camel), the sheep strain appeared to be the most common genotype of E. granulosus affecting sheep and goats. All of the 30 sheep samples and 20 out of 30 goat samples were infected with sheep strain. However, the camel genotype was only observed in the goats and 10 out of 30 goat isolates were infected with the camel genotype. The camel genotypes had RFLP patterns, which were different from the RFLP patterns of the rest of isolates (sheep strain). CONCLUSIONS: The results of this study revealed that the ‘sheep’ strain was the most prevalent strain in sheep and goats in this area. Moreover, the camel genotype (G6) was confirmed to trigger infection in the slaughtered goats of Birjand area.