The Sydney rock oyster (Saccostrea glomerata) is a commercially important bivalve in southeastern Australian. We describe the isolation and characterization of nine microsatellite markers for S. glomerata. The loci are highly polymorphic, with between five and 20 alleles identified among 30 individuals. Expected heterozygosity levels ranged from 0.608 to 0.936. The markers will be used to study natural dispersal, translocations and population structure. We will also use the microsatellites to test the genetic effects of QX disease on oyster populations. This infectious parasitic disease has decimated S. glomerata productivity in a number of areas over the past few decades.