Given the high degrees of adaptation to specific microhabitats and restricted-range endemism, Goniurosaurus (Tiger geckos) serves as a unique model to study the complex evolution in lizards. Using phylogenetic analyses, we estimated the first divergence date of Goniurosaurus to the Eocene (~ 45.3 mya). The diversification within four monophyletic species groups began in the mid-Miocene between ~ 13.4 and 7.7 mya and continued to at least the early Pleistocene (~ 2 mya). Their ancestor was predicted to originate somewhere in contiguous continental Eastern Asia, whereas the current regions in which each monophyletic Goniurosaurus species group radiated are respectively their own ancestral regions. Together with factors of altitudinal gradient and climate conditions, we reconstructed relevant niche models of Goniurosaurus including ancestral reconstructions. Consequently, low elevations were predicted to be the most probable ancestral state for Goniurosaurus and all its groups as well. Both climatic niche conservatism and divergence have shaped the extraordinary species richness of allopatric Chinese and Vietnamese tiger geckos. In terms of endangerment, Goniurosaurus has been considered one of the most susceptible lizard groups under severe human impacts, especially climate change. The assessments of their niche evolution can provide a science-based pre-signal of vulnerability, thereby improving the efficacy of conservation measures to safeguard species of Goniurosaurus in the future. Accordingly, almost all closely related species of Goniurosaurus in China and Vietnam were identified with a high rate of niche conservatism, which should be included in conservation priorities under potential impacts of climate change.