Next Generation DNA sequencing was used to develop a suite of microsatellite markers for the marine mollusk, Donax deltoides. A total of 20 polymorphic loci were identified and 12 characterized using 30 individuals from a single population (Venus Bay) in south eastern Australia. We observed moderate to high genetic variation across most loci (mean number of alleles per locus = 7.3; mean heterozygosity = 0.633) with only a single locus (Ddel32) displaying significant deviation from Hardy-Weinberg equilibrium. Marker independence was confirmed with tests for linkage disequilibrium, however two loci were found to be influenced by null alleles. The 10 viable markers characterized in the present study provide a valuable resource for future population genetic assessments and fisheries management of D. deltoides in Australia.