Aim: Savanna biomes cover around 20% of land surfaces, yet the origins and processes that have shaped their biodiversity remain understudied. Here, we assess the timing of diversification and how patterns of genetic diversity vary along an aridity gradient in specialized saxicoline gecko clades (Oedura spp.) from the tropical savannas of northern Australia. Location: Australian Monsoonal Tropics (AMT), Kimberley region (Western Australia). Methods: We compiled mitochondrial and nuclear data for two Kimberley endemic lizard clades (Oedura filicipoda/murrumanu and O. gracilis), and allied non-Kimberley taxa (O. marmorata complex). Species delimitation methods were used to identify evolutionary lineages, Maximum-likelihood and Bayesian phylogenetic methods were employed to assess relationships and diversification timeframes, and rainfall data and range sizes were tested for correlations. Results: Phylogenetic analyses of cryptic or recently discovered lineage diversity revealed late-Miocene to early-Pliocene crown ages. Microendemism and diversity were highest in high-rainfall regions, while the most widespread lineages occurred in the central and south-east Kimberley, and showed evidence of introgression with parapatric lineages. Main conclusions: The initial diversification in both clades was broadly concordant with global climatic events linked to the expansion of savanna biomes in the late-Miocene. Higher endemism in mesic and refugial areas suggests long histories of localized persistence, while wider distributions and evidence of introgression suggest a dynamic history at the arid-monsoonal interface.