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Background: Hydatidosis is one of the most important zoonotic parasitic disease worldwide caused by Echinococcus granulosus. Given the importance of parasite genotyping in disease control, this study was aimed to evaluate the genetic variation of the camel and dog isolates in Isfahan. Material and Methods: This cross-sectional study was done on infected livers and lungs of camels with hydatid cyst (n=51) during 2015-2016, collected from Zarinshahr and Najafabad industrial abattoir and 200 adult E. granulosus worms collected from stray dogs in different geographical regions of Isfahan for the molecular identification of mitochondrial genes (CO1, ND1). The DNA of protoscolices and adult worms were extracted, the PCR and sequencing were done using specific primers. Pairwise sequence alignment was used to identify the genetic similarity between the sequences and the registered ones in Gen bank using Clustalw2 software. Results: The PCR and sequencing of CO1 and ND1 genes on dog and camel samples showed different E. granulosus genotypes, including the common sheep strain (G1), bovid strain(G3) and camel strain (G6) in Isfahan region. The most frequent strains were the common sheep strain (G1). The genetic similarity between both ND1 and CO1 isolates taken from camel, dog and the isolates registered in Gene bank were 30.25-100% and 27.47-100% for camel and dog, respectively. Conclusion: Mitochondrial ND1 and CO1 genes are proper molecular markers for identifying the genetic variation of the camel and dog E. granulosus. The dominant strain of the worm in Isfahan, is the same as the other parts of the country, i.e., the G1 genotype (the most common sheep strain) belonged to the G1- G1 E. granulosus complex.