We describe a new species of agamid lizard, Ctenophorus mirrityana sp.nov. currently known from two disjunct populations in western New South Wales. The species is a member of the C. decresii species complex, and was formerly recognized as an outlying population of C. decresii due to similarities in dorsal colour pattern and adjacent distributions. Previous work documented deep molecular divergence, across multiple loci, with no genetic admixture between the new species and proximal C. decresii populations. We find that the new species differs in morphology from all other members of the species complex and is characterized by distinct male throat and lateral coloration, a small head size relative to snout-vent length, a large number of labial scales, and a lack of tubercular scales. We also identify two geographically structured lineages (northern and southern) within C. decresii as requiring further taxonomic investigation, based on notable genetic and morphological (including colour) divergence. We find that divergence in coloration is associated with genetic and body form differentiation within the C. decresii species complex.