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The intermediate horseshoe bat (Rhinolophus affinis) is a widespread species in Southeast Asia. We developed 19 novel microsatellite loci from an enriched genomic library of the bat, and tested their polymorphism using a single population from Guangdong province, southern China. The number of alleles ranged from 3 to 15 per locus with the expected and observed heterozygosity ranging from 0.397 to 0.920 and 0.280-0.926, respectively. Three markers significantly deviated from the Hardy- Weinberg expectations after Bonferroni correction and no linkage disequilibrium was detected in any of loci. These microsatellite loci will be useful in studying the phylogeography of this species. [ABSTRACT FROM AUTHOR]