West-central China is an important endemic focus of both alveolar and cystic echinococcosis where several species of intermediate host are commonly infected with Echinococcus granulosus and E. multilocularis . Isolates of E. granulosus were collected from humans and other animals from different geographical areas of Qinghai, Ningxia, Gansu and Sichuan, and genotyped using the mitochondrial DNA marker ATP synthase subunit 6 gene (atp6). The sheep strain (G1 genotype) of E. granulosus was shown to be the only genotype present in sheep, cattle, goats, yaks and humans in the study areas. However, some heterogeneity in the atp6 sequence was evident in a number of the isolates with the most frequent change being a silent substitution (G/A) at position 360 compared with the G1 reference sequence representing isolates collected from the majority of hosts except humans. Two E. multilocularis isolates examined also had sequences that varied from each other and from the reference E. multilocularis atp6 sequence. The genotypic variation we report may reflect phenotypic differences with important consequences in terms of increased host infectivity for hosts by local Echinococcus strains, possibly impacting on the epidemiology and control of echinococcosis. Such adaptations may also result in different sensitivity to drugs or increased virulence for hosts that will impede control efforts and even affect vaccination strategies against Echinococcus.