We tested for parentage verification and mating systems in Pseudois nayaur in Helan Mountain Rock Painting Scenic area. 369 fresh faecal samples were collected from July to August and November to December 2017. All faecal samples were then tested through genotyping, using 10 microsatellite loci that had relatively high polymorphism. A total of 282 individuals (152 males and 130 females) were identified through compound amplification and amelogenin gene (AMELX & AMELY) PCR. A total of 101 alleles were detected in 10 microsatellite loci and the average number of alleles (Na) was 10.1, while the mean observed and expected heterozygosities were 0.7737 and 0.6512. Furthermore, the mean value of polymorphic information contents (PIC) was 0.6129. Parentage verification was conducted on Cervus 3.0. Kingroup V2 and was used to calculate the coefficient of relationship (r) between individuals as a supplement to parental identification. The results showed that there were 7 parentage groups, 21 father-child groups and 19 mother-child groups. Based on the analysis of these relationships, we deduced that Pseudois nayaur have a polygynous mating system.