454 Next Generation sequencing was used to develop a set of microsatellite markers for the Great Artesian Basin (GAB) amphipod, Wangiannachiltonia guzikae. Primers were designed for 42 microsatellite loci. A total of 22 loci were successfully amplified and 16 characterised using 30 individuals from a single GAB spring population. Across these 16 loci, observed heterozygosity ranged from 0.000 to 0.818 (mean = 0.445) and the number of alleles per locus ranged from 2 to 12 (mean = 6.688). Of these 16 loci, however, only 10 were in Hardy–Weinberg equilibrium, though all 16 loci should be retained for further studies in the event that stochastic events affected equilibrium of this single population.