Thirteen microsatellite loci were developed and characterised for two fishes from temperate Australia that exhibit atypical diadromous migration strategies. Cloning and sequencing of an enriched partial genomic library was used to develop seven highly polymorphic loci for the catadromous species Pseudaphritis urvillii (known as tupong or congolli). Mean number of alleles per locus was 16. 5, and average observed and expected heterozygosity was between 0. 90 and 0. 87, respectively. Six polymorphic markers characterised for the anadromous species Lovettia sealii (known as Tasmanian whitebait) included a mean of 12. 3 alleles per locus and average observed and expected heterozygosity of 0. 71-0. 77, respectively. These microsatellites will be employed to understand regional patterns of recruitment, migration and stock structure.