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Echinococus shiquicus as a new member of the genus Echinococcus has been reported in Sichuan Province,China.Its definitive host was Tibetan fox (Vulpesferrilata) and the intermediate host was plateau pika (Ochotona curzoniae).The parasitic sites of the larval stage in the intermediate host were lungs and liver,but there was no report that other organs,such as spleen and kidney could be the parasitic sites ofE.shiquicus metacestode.In this study,80 plateau pikas were examined from Qinghai:Tibet Plateau showing that the cysts can exist in the spleen and kidney.Specific:species PCR primers were designed for identifying the species,then we designed other two primers based on the complete mitochondrial genome for amplifying the whole segments of the NADH dehydrogrnase subunit 1 (nad1) gene and the cytochrome C oxidase subunit 1(cox1) gene.Neighbour:joining (N J) method was used to construct phylogenetic tree by MEGA 5.2.1 software based on the nad1 and cox1 sequence,then we also counted the genetic diversity.All our results indicated the cysts in the spleen and kidneywhich we found in plateau pikas were belong to E.shiquicus and there were hardly genetic diversity between different parasitic sites and intermediate hosts.