Black nerite snails are ecologically important herbivores of the intertidal zone of Australia's temperate marine coast. A set of 13 microsatellites was developed for the black nerite Nerita atramentosa using 1/8 of a shot-gun pyrosequencing reaction. From 46,971 sequences containing putative microsatellite motifs, 18 were selected for primer design. Thirteen microsatellite loci were successfully genotyped using three multiplex reactions in 45 specimens of black nerite from two localities. The number of alleles per locus varied from four to 23 (mean = 12.4) and the observed heterozygosity ranged from 0.40 to 0.96 (mean = 0.72). Only one locus showed significant deviation from Hardy-Weinberg equilibrium probably due to null alleles. No linkage disequilibrium between pairs of loci was detected. These polymorphic markers represent useful tools for connectivity and seascape genetic studies of Australian black nerites. These studies should provide valuable information for the design and assessment of marine protected areas in temperate waters of Australia.