Eleven polymorphic microsatellite loci were isolated and characterised from sooty grunter (Hephaestus fuliginosus) and Tully grunter (H. tulliensis) from Northern Australia. Each primer pair amplified good quality and polymorphic products. The versatilities of these markers were tested using different H. fuliginosus populations and cross-amplified to a closely related species, H. tulliensis, found within the northern Australian wet tropics. The number of alleles ranged from 5 to 20 per locus and expected heterozygosities ranged from 0.043 to 0.926. All loci conformed to Hardy-Weinberg expectations, with the exception of 2Hf44 and 2Hf53 for Daly R. and Mitchell R. populations of H. fuliginosus, respectively. No evidence of linkage disequilibrium was detected between any pair of loci. The markers reported here would be very useful for population genetic studies, evolution and conservation of these species.