Although already famous for their richness, the biodiversity of most tropical biomes is likely to be underestimated by current taxonomy, especially for low dispersal species. Combining extensive field work, new tools from phylogenomics, and analyses of phenotypes and distributions, we have focused on the lizard fauna across the vast monsoonal savanna of northern Australia. Though well characterized by traditional morpho-taxonomy, we have uncovered extreme levels of mostly cryptic phylogeographic diversity in skinks and geckos – on par with that seen previously in rainforests. Deciding how to delineate species vs intraspecific lineages in these systems is challenging, but an integrative approach suggests that typically only the most phylogenetically divergent lineages warrant recognition as species. Along with evidence of genetic introgression, this points to the protracted nature of cryptic speciation in this system. To represent this hierarchical diversity, below and above species level, we have applied phylogenetic diversity measures across taxa, revealing new hotspots of phyloendemism and conservation priorities. These results are informing priorities for conservation management by government agencies, NGOs and Indigenous communities with whom we collaborate.