The hog deer (Axis porcinus) is a small deer whose natural habitat is the wet or moist tall grasslands in South and Southeast Asia. Wild populations have dramatically decreased in recent decades. While wild hog deer were recently acknowledged to be extinct in China, a few captive populations have been maintained. In the present study, we successfully employed the restriction-site-associated DNA sequencing (RAD-seq) technique to generate a genome-wide profile of single-nucleotide polymorphisms (SNPs) in the captive population of hog deer from Chengdu Zoo, China (N = 11). Up to 4.7 million clean reads per sample were sequenced, and 11,155 SNPs and 8,247 haplotypes were simultaneously observed within more than 80% of sequenced individuals. In this population, the mean frequency of major alleles at each polymorphism site was 0.7903±0.0014, and the average nucleotide diversity (π) and inbreeding coefficient (FIS) were 0.3031±0.0015 and -0.0302±0.0062, respectively. Additionally, the Euclidean distance-based multidimensional scaling method revealed that the pairwise genetic relatedness was evenly distributed. However, the results of homologous searching by short reads did not provide any meaningful explanation of the phylogenetic relationship of hog deer, which should be further investigated. In conclusion, our results revealed current state of genetic diversity in this captive population of hog deer.Furthermore, these genome-wide SNPs would be useful for guiding the mating schedule to avoid sharp increase of inbreeding coefficient.