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Australia's lizard fauna is among the most diverse in the world. Yet for the continent's vast northern Monsoonal Tropics, recent genomic and morphological evidence indicate that current taxonomy significantly underestimates actual biological diversity. Apparently widespread species typically contain ancient phylogenetic divisions or confounded taxonomic boundaries. Resolving the distributions and relationships across tropical species complexes reveals higher diversity than is recognised taxonomically and may warrant substantial taxonomic changes. For conservation assessments however, we need not wait for revised taxonomy, because phylogenetically informed analyses can use the best available data to inform conservation priorities now, independent of taxonomy. We present results of a large-scale conservation analysis based on comparative phylogeography of ten genera of lizards in two families (Gekkonidae and Scincidae) across the “Top End” of northern Australia, an ecologically and topographically diverse landscape recognised for its high biodiversity and indigenous cultural values. We combine the distributions and phylogeny of evolutionary lineages across multiple species complexes to estimate phylogenetic endemism, a measure of the extent to which evolutionary diversity is geographically concentrated. We demonstrate new methods for conservation assessment to incorporate phylogenetic diversity both within and across species, and for cases where taxonomy is uncertain or incomplete. We identify five hotspots of endemism, some previously known such as the Arnhem Plateau but others that are newly identified such as the Wessel & English Company Islands and the Darwin-Litchfield area. We find that, weighted by range size, the 28% of the region within protected areas holds 44% of the region's sampled phylogenetic diversity.