Simple SummaryDiseases caused by parasites have introduced serious threats to human health and the development of animal husbandry in the Qinghai–Tibetan Plateau Area (QTPA), such as toxoplasmosis caused by Toxoplasma gondii and neosporosis caused by Neospora caninum. However, information on the epidemiology of toxoplasmosis and neosporosis in stray cats and dogs which are the definitive hosts of T. gondii and N. caninum in the QTPA is limited. The aim of this study was to establish a detailed record of the seroprevalence of T. gondii and N. caninum-specific IgG and IgM antibodies in serum samples and the molecular epidemiology in feces from stray cats and dogs in the plateau area. The results revealed that stray cats and dogs in the QTPA, China present both T. gondii and N. caninum infection through the antibodies and antigen detection of the indirect ELISA tests and qPCRs. The present study suggests the prevalence of acute neosporosis and chronic re-emergence of toxoplasmosis in stray cats and dogs in the testing area. To the best of our knowledge, this is the first report of T. gondii and N. caninum infection in cats and dogs in the QTPA, and the first determination of N. caninum infection in cats in China. In conclusion, stray cats and dogs play key roles in the transmission and prevalence of T. gondii and N. caninum in the plateau area.Toxoplasma gondii and Neospora caninum belong to the Apicomplexan protozoa which is an obligate intracellular parasite, causing toxoplasmosis and neosporosis throughout the world. Cats and dogs are the definitive hosts of these two parasites. However, information on the epidemiology of toxoplasmosis and neosporosis in stray cats and dogs in the Qinghai–Tibetan Plateau Area (QTPA) is limited, and little is known about the diversity of the diseases. Therefore, the aim of this study was to perform indirect ELISA tests based on recombinant TgSAG1, TgGRA1, NcSAG1 and NcGRA7 proteins to establish a detailed record of the seroprevalence of T. gondii and N. caninum-specific IgG and IgM antibodies in serum samples and to develop qPCR amplification based on TgB1 and NcNc5 genes to conduct molecular epidemiology in feces from stray cats and dogs in the QTPA. In the current study, a total of 128 cat serum samples were analyzed through serological tests in which 53 (41.4%) and 57 (44.5%) samples were found positive for T. gondii specific-IgG and IgM antibodies, and 2 (1.6%) and 74 (57.8%) samples were confirmed positive for N. caninum specific-IgG and IgM antibodies, respectively. Out of 224 stray dog sera, 59.8% and 58.9% were recorded as positive against anti-Toxoplasma IgG and IgM antibodies, 17.9% and 64.7% were detected positive against Neospora IgG and IgM. On the other hand, 1 of 18 cat fecal samples was successfully amplified within the Ct value of 10 to 30 while no cat was positive for neosporosis. Moreover, a higher prevalence of toxoplasmosis in stray dogs (14.5%, 16/110) than of neosporosis (5.5%, 6/110) with different parasite numbers were found. Further analysis showed that no significant sex differences were found nor between the overall infection rates of T. gondii and N. caninum in this study. This study suggests that stray cats and dogs play key roles in the transmission and prevalence of T. gondii and N. caninum in the plateau area.