Echinococcus granulosus is the causative agent of cystic echinococcosis with medical and veterinary importance worldwide. The aim of this study was to determine the genotype distribution of E. granulosus in animals in Yushu, Qinghai Province, northeastern China. The mitochondrial nicotinamide adenine dinucleotide+hydrogen (NADH) dehydrogenase subunit 1 (nad1) and cytochrome c oxidase subunit 1 (cox1) genes from 30 echinococcosis isolates were analyzed by sequence alignment, generating two unique sequence profiles at both nad1 and cox1 loci. Phylogenetic analysis demonstrated that 28 isolates (93.3%) belonged to the well-known G1-G3 complex (E. granulosus sensu stricto), and 2 (6.7%) were placed in G6-G10 complex (E. canadensis). The present study provides the genetic composition of E. granulosus from animals in Yushu, Qinghai Province, and confirms that, for the first time, the E. granulosus G6-G10 complex (E. canadensis) is not only limited to Xinjiang and might be of greater public health significance than previously believed in China.