The dramatic increase in scale allowed by next-gen sequencing coupled with emerging coalescent-based analysis methods offers great scope for increasing our understanding of biodiversity pattern and its evolutionary foundations. We have combined mtDNA phylogeography with sequence and SNP data for 1000s of loci obtained via custom exon capture to uncover the diversity of widespread lizard taxa across Australia’s tropics. The results indicate that traditional morphology-based taxonomy underestimates diversity several-fold, especially in geckos. Mapping of phyloendemism confirms several well-known biodiversity hotspots, but also reveals new ones, especially on islands and in presumed climatic refugia in areas with harsher climates. Much of this diversity occurs in indigenous managed lands, which have higher biodiversity value than currently realised. In some areas, initial results point to a high frequency of past introgression across multiple taxa. Understanding how speciation-extinction dynamics have shaped these various patterns remains a challenge, and we propose that stability of local micro-climates has played a key role. If so, this bears on how landscapes are managed for conservation