Twenty microsatellite loci developed for the straw-colored fruit bat, Eidolon helvum, are described. These markers were used in multiplex PCRs to amplify genomic DNA from 142 individuals sampled from nine populations across Africa. Nineteen loci were polymorphic, with a mean number of alleles per locus of 16.2 (3–46). Observed and expected heterozygosity values ranged from 0.01 to 0.90 and 0.03 to 0.97, respectively. These markers will be used in combination with mitochondrial DNA sequences to investigate gene flow and the genetic meta- population structure of E. helvum.