he western rainbowfish (Melanotaenia australis) is one of the most common and highly abundant freshwater fish endemic to north-western Australia. It shows extensive geographic variation in their colour pattern. Genetic study revealed spatial population structure in this species that could be a possible threat to its existence. Therefore we designed and isolated 15 highly polymorphic microsatellite markers for M. australis for use in population studies across its distribution. We screened these primers across 32 individuals from the Daly River and found between 4 and 22 alleles per locus. The observed heterozygosities ranged from 0.345 to 1.000. These markers will be now available for future studies of population structure across its natural range and to assist in management as well as future conservation.