Abstract: Currently, there is a lack of systematic research on the population size prediction of Cervus elaphus in the Ebinur Lake Wetland National Nature Reserve in Xinjiang. To understand the population size and trends of Ce. elaphus in Ebinur Lake Nature Reserve, 220 fresh Ce. elaphus fecal samples were collected from July 2023 and May 2024. Based on non-invasive sampling methods, 11 microsatellite loci and the SRY/BMC1009 gene were used for individual identification and sex determination. The results showed that 86 genetically distinct Ce. elaphus individuals were identified from 220 fecal samples, with a sex ratio of 1.15:1 (46 females: 40 males). Further assessment of the Ce. elaphus population in Ebinur Lake Nature Reserve using non-invasive mark-recapture (CMR) indicated an estimated population size of approximately 138 individuals, representing an increase compared to previous studies. This molecular-based investigation into the population size and sex ratio structure of Ce. elaphus in Ebinur Lake Nature Reserve provides scientific evidence for refining species information within the reserve and formulating scientifically sound population conservation strategies.