Limb-reduced and limbless scincid lizards pose problems in untangling their relationships because of a strong tendency toward convergent evolution in which functional characters mask phylogenetic history. Their often small size makes cranial characters difficult to study, and collections of such species are often small and patchy because of their cryptic behavior. One such genus, Anomalopus (Sphenomorphinae), currently includes seven species of reduce-limbed and limbless skinks that occur in tropical and subtropical habitats in eastern Australia. The discovery of previously unreported populations of limbless skinks assignable to Anomalopus has prompted our revision of the morphology and systematics of this genus. We report new DNA sequence data and new morphological data by using X-ray micro-computed tomography scanning that corroborate published molecular data on sphenomorphine phylogeny, leading us to propose a new generic arrangement that recognizes the species of Anomalopus as belonging to three genera. The newly discovered populations represent two new species currently known from only three small and disjunct areas. We review the osteology of the three genera of the former Anomalopus, finding new characters and variable patterns of interspecific and interclade variation. The same morphological characters are modified in every limb-reduced sphenomorphine clade, but to differing degrees and in different combinations in each.