We describe a microsatellite panel of 12 newly developed and four cross-amplification loci for the endangered Australian sea lion, Neophoca cinerea. Next-generation 454 sequencing was used to obtain species-specific partial genomic library. We genotyped 28 individuals sampled from a single breeding colony to characterize these 16 polymorphic loci. Number of alleles per locus ranged from three to seven, and observed and expected heterozygosites from 0. 333 to 0. 852 and from 0. 377 to 0. 787, respectively. These markers will be used to examine genetic diversity, genetic connectivity among colonies and the mating system of Australian sea lions.