Exploring phylogeographic patterns along south-western Angola reveals cryptic diversity within the Pachydactylus angolensis complex

South-western Angola hosts exceptional reptile diversity, yet the evolutionary processes driving this richness remain poorly understood. Here, we integrate phylogenetics, morphological analyses, and ecological niche modelling (ENM) to reassess species’ limits and diversification within the Pachydactylus angolensis complex, the only strictly endemic Pachydactylus species complex in Angola. Time-calibrated phylogenies based on mitochondrial and nuclear markers reveal four deeply divergent mitochondrial lineages, which diversified during the Late Miocene (∼10 Mya), each associated with a distinct ecoregion and displaying 15%–21% ND2 divergence. Morphological traits show strong conservatism but exhibit subtle differences in cranial structure, tooth loci arrangement, body size, and dorsal coloration. Furthermore, the analyses of three nuclear genes (RAG-1, KIAA, and c-mos) suggest mito-nuclear discordance within the ‘coastal’ clade, possibly reflecting secondary contact following historical climatic oscillations. Aiming to better understand such mito-nuclear discordances we generated past climatic ecological niche models, which support long-term segregation during glacial periods and partial overlap during interglacials, consistent with cycles of isolation and expansion. Based on these results, we describe an endemic species from west-central Benguela Province, Pachydactylus leucocephalus sp. nov., and designate the southern ‘coastal’ lineage as a candidate species pending additional evidence. Our findings highlight previously unrecognized cryptic diversity and illustrate the importance of continued fieldwork and genomic research to refine species boundaries and set conservation priorities in Angola.