Objective The development of polymorphic microsatellite markers of A.peninsulae can enrich the genetic data of A.peninsulae and lay a foundation for genetic quality control and gene mapping of A.peninsulae.Based on genomic data, microsatellite loci of A.peninsulae were developed for genetic quality analysis of A.peninsulae and enriched the genetic data of A.peninsulae. Methods Microsatellite loci were screened based on the genome sequence of Apodemus peninsulae, and microsatellite primers were mined. The genetic diversity of the population were analyzed by multiplex PCR. Results Thirty microsatellite markers were successfully developed, and 30 microsatellite loci were evaluated using 60 samples of Apodemus peninsulae. A total of 152 alleles were detected, with an average number of observed alleles of 5.067. The average observed heterozygosity was 0.592. The average Shannon index was 1.2645 ; the average polymorphism information content ( PIC ) was 0.598. Conclusions Based on the microsatellite loci developed in this study, the genetic diversity of A.peninsulae population can be effectively analyzed, which lays a foundation for the establishment of genetic quality standards and genetic quality detection methods of A.peninsulae.