Galaxias maculatus (common Galaxias, jollytail, inanga, Puye, Falkland’s minnow) is the world’s most naturally widespread freshwater fish with an intercontinental distribution that ranges from Western Australia eastwards as far as the Falkland Islands. The species is amphidromous with marine dispersed larvae and saline tolerant adults but readily establishes non-diadromous populations in isolated inland water bodies. Landlocked populations show characteristic changes in morphology including reductions in vertebral number and increased numbers of gill rakers and have often been described as separate species. We have examined the population genomics of this species using a genotyping by sequencing approach evaluating 3800 single nucleotide polymorphisms in landlocked and diadromous populations from Tasmania, mainland Australia, New Zealand and the Falkland Islands. The resulting data supports expectations of genomic divergence based on geographic separation and the duration of inland isolation. Further analysis of the SNP data will examine convergent genomic selection associated with the loss of diadromy in inland populations.