Cryptosporidium is a parasitic protozoan that can infect a wide range of animals across different geographical areas. The current incidence of Cryptosporidium infection in yaks in Chamdo remains uncertain. Our objective was to determine the prevalence of Cryptosporidium in the study areas through the use of both serology and molecular inquiry. The ELISA and nested-PCR techniques were utilized to analyze blood (n=691) and fecal samples (n=91) from yaks obtained from various farms over the specified period. The nucleic acid-based analysis focused on the 18S rRNA gene. The ELISA approach indicated that the total prevalence of Cryptosporidium infection was 12.7%. The prevalence of Cryptosporidium in fecal samples, as revealed by nPCR, was 33.0% (30 out of 91). The sequencing of selectively amplified samples revealed the presence of C. bovis (n=5) and C. parvum (n=2). The study utilized logistic regression analysis to examine the correlation between Cryptosporidium infection and the yak's location (farms), health condition, age, and sex. The findings indicated that age, farm (with varying management practices), and health status were risk factors that influenced the frequency of Cryptosporidium in animals in Chamdo. Overall, the results gained help to develop control methods for Cryptosporidium infections in yaks.