Delimiting cryptic species is important in understanding the true biodiversity of an ecosystem and subsequently reflecting these cryptic species in conservation, management and policy. Current molecular evidence suggests that the broadly distributed genus of fish Mogurnda harbours high levels of cryptic biodiversity. The present study uses a large single nucleotide polymorphism (SNP) dataset to clarify taxonomic uncertainty, patterns of introgression and biogeographic patterns of Mogurnda within the Wet Tropics region. PCoA analysis separated taxa into two divergent Northern and Southern groups. Stepwise analysis revealed six taxa were present in the two groups. Heterozygosity values were variable by individual based on their taxa but were informative for the exclusion of eight introgressed individuals. Both maximum likelihood and SVDqaurtets trees supported these taxa, with high bootstrap support for all nodes (> 95%). Fixed differences were high between all taxa but were greater between taxa from different groups when compared to those within groups. All analyses support the delimitation of Mogurnda in the Wet Tropics into six new putative species, with four species being endemic to a single drainage. Based on this analysis, morphological appraisal is recommended to describe these six taxa as species within the genus Mogurnda. Biogeographically there was evidence for shared faunal exchange between the Herbert and North Johnstone catchments. It is likely that the genus Mogurnda across northern Australia has high levels of cryptic biodiversity and requires morphological comparison to revise their taxonomy.