Abstract: The red deer population in the Ebinur Lake Nature Reserve is distributed across the Ebinur Lake Wetland National Nature Reserve in Xinjiang (hereinafter referred to as the“Ebinur Lake Nature Reserve”). Currently, there is a lack of systematic research on the population size prediction of red deer in the Ebinur Lake Reserve. To understand the population size and trends of red deer in the Ebinur Lake Reserve, this study employed non-invasive sampling methods using 220 fresh red deer fecal samples collected between July 2023 and May 2024. Individual identification and sex determination were conducted using 11 microsatellite loci and the SRY/BMC1009 gene. Results revealed that the 220 fecal samples identified 86 genetically distinct red deer individuals, with a sex ratio of 1.15:1 (46 females: 40 males). Further assessment of the red deer 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 red deer in Ebinur Lake Nature Reserve provides scientific evidence for refining species information within the reserve and formulating scientifically sound population conservation strategies.