IntroductionGiardia and Leishmania are important zoonotic parasites, yet their transmission dynamics in wildlife hosts on the Qinghai-Tibet Plateau remain unclear. As a keystone species on the Plateau, Ochotona curzoniaes overlap spatially with livestock and human activity areas and may serve as potential reservoir hosts for these pathogens. However, relevant molecular epidemiological data are currently lacking.MethodsTo address this knowledge gap, the present study investigated the prevalence and molecular characteristics of Giardia and Leishmania in 114 O. curzoniaes collected from five townships in Zoige County, China, between March and December 2023. Intestinal contents and spleen samples were analyzed using nested PCR targeting Giardia bg, gdh, tpi genes and Leishmania ITS-1 gene. Positive products were sequenced, followed by BLAST comparison and phylogenetic analysis for species identification and genotyping.ResultsResults showed 50 samples were Giardia-positive (43.9%), including 44 bg-positive and 14 gdh-positive samples, with eight samples positive for both genes. Five samples (4.39%) were positive for Leishmania. Significant differences in Giardia prevalence among the five locations were observed, whereas Leishmania prevalence did not differ significantly. Phylogenetic analysis identified G. intestinalis assemblage E (n = 38), G. microti (n = 6) based on bg, and a potentially novel genotype, tentatively designated Giardia sp. clone Z5 (n = 14) based on gdh. All Leishmania isolates were identified as L. major (n = 5).DiscussionThis study provides the first evidence of G. intestinalis assemblage E, G. microti, Giardia sp. clone Z5, and L. major in O. curzoniae, highlighting their role as potential wildlife reservoirs and supporting ongoing surveillance and genotyping of zoonotic protozoa in the Qinghai-Tibet Plateau.