Conflicting results from different molecular datasets have long confounded our ability to characterise species boundaries. Here we use genome-wide SNP data and an expanded allozyme dataset to resolve conflicting systematic hypotheses on an enigmatic group of fishes (Gadopsis, river blackfishes, Percichthyidae) restricted to southeastern Australia. Previous work based on three sets of molecular markers: mtDNA, nuclear intron DNA and 51 allozyme loci was unable to clearly resolve the status of a putative fifth candidate species (SWV) within Gadopsis marmoratus. Resolving the taxonomic status of candidate species SWV is particularly critical as based on IUCN criteria this taxon would be considered Critically Endangered. After all filtering steps we retained a subset of 10,862 putatively unlinked SNP loci for population genetic and phylogenomic analyses. Analyses of SNP loci based on maximum likelihood, fastSTRUCTURE and DAPC were all consistent with the previous and updated allozyme results supporting the validity of the candidate Gadopsis species SWV. Immediate conservation actions should focus on preventing take by anglers, protection of water resources to sustain perennial reaches and drought refuge pools, and aquatic and riparian habitat protection and improvement. In addition, a formal morphological taxonomic review of the genus Gadopsis is urgently required.