The species identification of an echinococcal lesion in the liver of a yak in the Qinghai-Tibet plateau region of China, where both Echinococcus granulosus and E. multilocularis are present, was difficult to determine because of the atypical appearance of the lesion. Polymerase chain reaction-based mitochondrial genotyping allowed us to discriminate the Echinococcus species. Nucleotide sequences of the cytochrome c oxidase subunit 1 (cox1) and cytochrome b (cytb) genes amplified from the echinococcal lesion demonstrated that the yak was infected with the E. granulosus G1 genotype (sheep strain).