Abstract Subspecies designations for herpetofauna in Western Australia were largely coined in the 20th century where rigorous evolutionary concepts to species were not consistently applied. Rather, subspecies tended to designate geographic populations of similar-looking taxa to nominate forms, usually differing in size, pattern or colour and, at best, a few scalation differences. Here we re-evaluate two pygopodoid taxa from Western Australia using a combination of published and original genetic data coupled with a reassessment of morphology. We review these differences in light of an integrative taxonomic approach that looks to find multiple independent lines of evidence to establish the evolutionary independence of populations. For the pygopod species Pletholax gracilis, we found consistent diagnostic characters (e.g. body size, visibility of ear opening, scalation) and a deep genetic divergence between the two subspecies. We therefore raise each subspecies to full species: P. gracilis and P. edelensis. The two subspecies of the carphodactylid gecko Nephrurus wheeleri were also assessed, and we found strong genetic and morphological evidence (e.g. body size, scalation, pattern) to raise these to full species: N. wheeleri and N. cinctus. By revisiting Storr’s morphological insights and newly acquired genetic evidence, in addition to a thorough re-examination of morphological traits, our study provides a robust foundation to raise Storr’s morphological subspecies into full species based upon multiple lines of evidence. Such an approach applied to other subspecies in the Australian herpetofauna also may result in revised taxonomies.