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The sympatric Apodemus species are excellent models for studying comparative phylogeography of organisms. On basis of the microsatellite development of three Apodemus species, we describe in this paper the isolation and characterization of microsatellite DNA markers in the two Apodemus species (Apodemus peninsulae and Apodemus latronum) from genomic DNA-enriched libraries. Ten and eight polymorphic loci were found in A. peninsulae and A. latronum, respectively. These loci were highly polymorphic with numbers of alleles per locus ranging from 11-20 and 6-16, and expected heterozygosity from 0.891-0.947 and 0.714-0.950 for A. peninsulae and A. latronum, respectively. Seven and six loci followed Hardy-Weinberg expectations for A. peninsulae and A. latronum, respectively. No significant linkage association was found among all these loci. These polymorphic microsatellite loci will be useful in studying comparative phylogeography of the sympatric Apodemus species.