Objective Polymorphic microsatellite markers developed for Apodemus peninsulae can enrich its genetic data and lay a foundation for genetic quality control and gene mapping. Methods Microsatellite loci were screened based on the genome sequence of Apodemus peninsulae, and microsatellite primers were identified. The genetic diversity of the population was analyzed by multiplex PCR. Results Thirty microsatellite markers were successfully developed and evaluated using 60 samples of Apodemus peninsulae. A total of 152 alleles were detected, with an average of 5. 067 alleles per locus. The average observed heterozygosity was 0. 592. The average Shannon index was 1. 265. The average polymorphism information content was 0. 598. Conclusions Based on the microsatellite loci developed in this study, the genetic diversity of Apodemus peninsulae can be effectively analyzed, laying a foundation for establishing genetic quality standards and detection method.