The white-bellied pangolin (Phataginus tricuspis) serves as a critical biogeographic indicator for understanding faunal diversification in African rainforests and is a priority for conservation due to its status as the most heavily trafficked and endangered mammal. However, the species' evolutionary history and the genetic consequences of population decline remain unclear. In this study, we conducted comprehensive phylogeographic and conservation genomic studies of 209 whole genomes, including 100 newly sequenced genomes, and 215 mitogenomes covering all geographic ranges. Our findings reveal four whole-genome genetic lineages and six mitochondrial genetic lineages, uncovering mito-nuclear discordance driven by deep mitochondrial divergence and the replacement of some mitochondrial lineages by nuclear lineages. We suggest that Pleistocene refugia and river barriers are hypothesized to have contributed to the pattern of genetic differentiation and biogeographic diversification. Demographic history reconstruction indicates that, historically, the population size dynamics were likely correlated with glacial-interglacial cycles. However, the recent sharp decline in population size can be attributed to overexploitation driven by international trade. The genetic consequence analyses and evolutionary potential simulation reveal that the Nigeria and West Africa lineages exhibit lower levels of genetic diversity, higher levels of inbreeding and genetic load, and lower survival status and future evolutionary potential, than the other lineages, indicating the need for urgent attention and priority conservation action. Our results provide novel insights into the evolutionary history and conservation priorities for white-bellied pangolins and offer a valuable phylogeographic and conservation framework for guiding conservation efforts to safeguard African rainforest biodiversity.