The eastern Qinghai-Tibet plateau of China is a highly endemic region of echinococcosis where Echinococcus granulosus sensu stricto (sheep strain), Echinococcus multilocularis, and Echinococcus shiquicus are distributed sympatrically. We developed a polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) method for the identification of the three species in this region. The PCR-RFLP showed the dual infection of animals with different Echinococcus spp. The first case was a domestic dog concurrently infected with adults of E. granulosus and E. multilocularis. The second case was a plateau pika (Ochotona curzoniae) harboring metacestodes of E. multilocularis and E. shiquicus in the liver. The high susceptibility of some mammalian hosts to the parasites and the high prevalence of the three co-endemic species probably increase the chance of mixed infections in the eastern Tibetan plateau.