The Australian banjo frogs are a distinctive group of medium to large, terrestrial, and burrowing limnodynastid frogs known for their conspicuous, single-note advertisement calls which are often likened to the pluck of a banjo string. Preliminary analyses of mitochondrial DNA sequences had previously indicated that the present taxonomy of the group, based primarily on morphology and advertisement calls, may not best reflect the true evolutionary relationships among taxa. In this study, we use comprehensive geographic sampling and integrative analyses of mitochondrial DNA sequences, nuclear single-nucleotide polymorphisms, adult morphology, and advertisement call data to re-evaluate the systematics and taxonomy of the Northern Banjo Frog (Limnodynastes terraereginae) and allied taxa. Our study reveals the presence of three evolutionarily distinct, morphologically divergent, and narrowly allopatric lineages that replace each other in a north–south series from the tip of Cape York Peninsula to the Sydney Basin in the south. Our findings demonstrate that our understanding of the systematics and taxonomy of Australian frogs remains incomplete, even for large and apparently “well-known” species that live in densely populated areas.