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Simple Summary: Estimation of population abundance or density is necessary for managing deer populations. However, there is no estimation of Siberian roe deer (Capreolus pygargus) in the Lesser Xing'an Mountains, northeast China where the density of roe deer is much lower than that of European or North American populations. We used fecal-DNA capture-mark-recapture to estimate the abundance and density in Liangshui National Nature Reserve. We collected 422 fecal pellet groups during two sampling periods in 2016, identified them to be 77 individuals by the DNA microsatellite technique and estimated the abundance of roe deer to be 87 deer (80–112, 95% CI) using the Program CAPTURE. Density was estimated to be 2.9 deer/km2 (2.7–3.7, 95% CI). Our study estimated the roe deer population abundance by a feces-based capture-mark-recapture approach in northeast China, successfully demonstrating the applicability of this feces sampling method in monitoring deer populations in this area. It also contributes to the development of low-density deer population ecology and management. It is necessary to estimate the population abundance of deer for managing their populations. However, most estimates are from high-density populations inhabiting the forests of North America or Europe; there is currently a lack of necessary knowledge regarding low-density deer populations in different forest habitats. In this article, we used fecal DNA based on the capture-mark-recapture method to estimate the population abundance of Siberian roe deer (Capreolus pygargus) in Liangshui National Nature Reserve in the Lesser Xing'an Mountains, northeast China, where the deer population was found to be of a low density by limited studies. We used a robust survey design to collect 422 fecal pellet groups in 2016 and extracted DNA from those samples, generating 265 different genotypes; we thus identified 77 deer individuals based on six microsatellite markers (Roe1, Roe8, Roe9, BM757, MB25 and OarFCB304). With capture and recapture records of these 77 individuals, the abundance of roe deer was estimated to be 87 deer (80–112, 95% CI) using the Program CAPTURE. Using an effective sampling area which resulted from the mean maximum recapture distance (MMRD), we converted the population abundance to a density of 2.9 deer/km2 (2.7–3.7, 95% CI). Our study estimated the roe deer population abundance by a feces-based capture-mark-recapture approach in northeast China, successfully demonstrating the applicability of non-invasive genetic sampling in monitoring populations of deer in this area, which contributes to the development of low-density deer population ecology and management. [ABSTRACT FROM AUTHOR]