Determining the connectivity of populations represented within marine protected areas (MPAs) is an essential element for understanding whether MPAs form effective networks. Trachinops caudimaculatus is representative of fish species with an extensive range encompassing multiple MPAs and provides an opportunity to estimate genetic connectivity along the southern coastline of Australia for these important taxa. A total of 13 microsatellites were developed using a 454-sequencing approach for T. caudimaculatus. All loci were found to be polymorphic, with the number of alleles detected ranging from three to 23 and observed heterozygosity ranging from 0.15 to 0.91. These markers will be used to assess the genetic diversity and connectivity throughout the range of T. caudimaculatus.