Cervus nippon hortulorum was once considered to be extinct in the wild. In recent years, some small size populations were found in the southeastern part of Heilongjiang province and the eastern part of Jilin province, nearing the border. Since the habitats of C. n. hortulorum are narrow, isolated and fragmented, it is an urgent need to further evaluate the genetic changes of the population, especially the genetic diversity and inbreeding decline, so as to enhance the pertinence of conservation and management. In this study, 673 suspected fecal samples of sika deer were collected from 9 key research areas in Daxing'an, Xiaoxing'an and Changbai Mountains (Fig. 1). Firstly, species identification was carried out based on DNA Cyt b gene sequencing technology, and the positive samples were supplied for further individual identification by microsatellite technology. At last, Microchecker 2.2.3 software was used to detect the invalid allele or allele deletion of each locus; and Genalex 6.0 software was used to calculate the population average allele number (Na), observed heterozygosity (Ho), expected heterozygosity (He) and fixed coefficient (Fis). A total of 33 individuals (20 in Muling nature reserve and 13 in Laoyeling nature reserve) were identified from 106 fecal DNA samples of sika deer (Fig. 2 and Table 1). Six variation sites and five haplotypes were detected in the Cyt b sequence of these 33 individuals. The values of Hd, Pi, Na, Ho, He and Fis were 0.621, 0.006 7, 7.1, 0.604, 0.712, and 0.152, respectively (Table 1). The results showed that the population genetic diversity of Northeastern sika deer was rich, but there was also a certain degree of heterozygosity deficiency and inbreeding (Table 1); the population experienced bottleneck effect in recent years, without population expansion (Table 1 and Fig. 5); there was no genetic differentiation between populations, which could be protected as a management unit (Table 2 and Fig. 3, 4). It is suggested that the individuals with rare haplotypes should be taken as the key point in monitoring and protection, and the artificial bred populations should be released in the field at the right time, so as to improve the gene exchange between individuals in the field and accelerate the population restoration.