To provide genetic tools for individual identification of the masked palm civet (Paguma larvata) through DNA analysis, we selected a tissue sample from Laohegou Nature Reserve in Sichuan for constructing microsatellite library by FIASCO. Altogether 250 clones were sequenced and 147 sequences were found containing microsatellite motifs, in which there were 42 sequences with >10 motif repeats. Primer pairs were designed based on these 42 sequences. Through tests for amplification and polymorphism using additional 21 samples of masked palm civets, 5 polymorphic microsatellite markers were obtained. In the meantime, 13 microsatellite markers published previously were tested for the masked palm civet, and found 5 of them polymorphic. Collectively, these 10 markers showed relatively high polymorphism (number of alleles was 2–11, observed heterozygosity was 0.286–0.737, and expected heterozygosity was 0.358–0.906). The values of PID and PID-sib indicated that there would be individuals with completely identical genotypes in about 10⁹ unrelated individuals or 10⁴ related individuals. As the size of wild populations in a particular region was greatly lower than this number, these 10 microsatellite markers were sufficient for individual identification for the masked palm civet.