Microsatellite technology was utilized in the present study to investigate paternity testing, mating system, genetic diversity, and population quantity of Chinese muntjac (Muntiacus reevesi) to increase the knowledge of relationships between members of the species, reproductive strategies, and evolution potential. Therefore, the present study aims to assist the facilitation of in-depth research and protection of the species. We collected 634 fecal samples and 2 muscle samples from Chinese muntjac (M. reevesi) in Gutianshan National Nature Reserve in January 2013 and April 2014. After repeated experiments, 8 microsatellite loci were selected, which had stable amplification and high polymorphism information, and 442 samples were utilized for polymerase chain reaction (PCR) amplification. Based on the preliminary identification in terms of the fecal morphology, a verification test was conducted with the mitochondrial cytochrome b gene (Cyt b), which was regarded as a supplement to the species identification. Individual identification for Chinese muntjac was conducted by contrasting the fingerprints synthesized by the eight microsatellite marker genotypes. The SRY gene was amplified at three times to reduce any false negative influence on the fecal samples, where the target band was identified as male when it appeared more than two times. The SRY gene and 8 microsatellite loci were utilized for sexual and individual identification, respectively, and 177 individuals, including 94 females and 83 males, were identified. The results showed that the total number of microsatellite alleles were 88, and the mean number of alleles was 11, ranging from 8 to 16, and the mean observed and expected heterozygosities were 0.9685 (0.960-1.000) and 0.8429 (0.799-0.887), respectively. The polymorphism information content ranged from 0.766 to 0.872, with an average of 0.821. Based on the above data, the Chinese muntjac population in Gutianshan National Nature Reserve has a high level of genetic diversity. The identification of 8 microsatellite loci identification rate from Cervus3.0 was 100%, when the confidence level was 95% and 80%. Among 24 parentage groups, 19 father-child relationships and 23 mother-child relationships were obtained among 104 individuals. The result of the relationship analysis showed that the mating system of Chinese muntjac belongs to a polygyny. However, it does not belong to any known subtypes, and this polygyny might be called a "check strategy". During the female reproductive period, once the female individual is pregnant she will not mate with any other males. However, the relationship is not fixed and the female might still mate with another male in the next breeding season. Therefore, in the present study, the mating phenomenon of a female and several males appeared in different breeding periods.