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We aimed to investigate the species composition of a small mammal community and the prevalence of <i>Echinococcus</i> spp. in a typical endemic area of the Tibetan Plateau. One pika and five rodent species were identified based on the morphological characteristics of 1278 small mammal specimens collected during 2014–2019. Detection of <i>Echinococcus</i> DNA in tissue samples from small mammal specimens revealed that <i>Ochotona curzoniae</i> (pika, total prevalence: 6.02%, 26/432), <i>Neodon fuscus</i> (5.91%, 38/643), <i>N. leucurus</i> (2.50%, 3/120), and <i>Alexandromys limnophilus</i> (21.74%, 10/46) were infected by both <i>E. multilocularis</i> and <i>E. shiquicus</i>; <i>Cricetulus longicaudatus</i> (16.67%, 1/6) was infected by <i>E. shiquicus</i>; and no infection was detected in <i>N. irene</i> (0/15). <i>Neodon fuscus</i> and <i>O. curzoniae</i> were the two most abundant small mammal species. There was no significant difference in the prevalence of pika and the overall rodent species assemblage (6.26%, 53/846); however, the larger rodent populations suggested that more attention should be paid to their role in the transmission of echinococcosis in the wildlife reservoir, which has long been underestimated. Moreover, although DNA barcoding provides a more efficient method than traditional morphological methods for identifying large numbers of small mammal samples, commonly used barcodes failed to distinguish the three <i>Neodon</i> species in this study. The close genetic relationships between these species suggest the need to develop more powerful molecular taxonomic tools.