Recent radiations are important to evolutionary biologists, because they provide an opportunity to study the mechanisms that link micro- and macroevolution. The role of ecological speciation during adaptive radiation has been intensively studied, but radiations can arise from a diversity of evolutionary processes; in particular, on large continental landmasses where allopatric speciation might frequently precede ecological differentiation. It is therefore important to establish a phylogenetic and ecological framework for recent continental-scale radiations that are species-rich and ecologically diverse. Here, we use a genomic (approx. 1 200 loci, exon capture) approach to fit branch lengths on a summary-coalescent species tree and generate a time-calibrated phylogeny for a recent and ecologically diverse radiation of Australian scincid lizards; the genus Cryptoblepharus. We then combine the phylogeny with a comprehensive phenotypic dataset for over 800 individuals across the 26 species, and use comparative methods to test whether habitat specialization can explain current patterns of phenotypic variation in ecologically relevant traits. We find significant differences in morphology between species that occur in distinct environments and convergence in ecomorphology with repeated habitat shifts across the continent. These results suggest that isolated analogous habitats have provided parallel ecological opportunity and have repeatedly promoted adaptive diversification. By contrast, speciation processes within the same habitat have resulted in distinct lineages with relatively limited morphological variation. Overall, our study illustrates how alternative diversification processes might have jointly stimulated species proliferation across the continent and generated a remarkably diverse group of Australian lizards.