Future global warming is one of the most significant threats facing the persistence of current biodiversity (community, species and genes). Consensus now predicts widespread shifts in regional climates due to changes in temperature, rainfall, seasonality and disturbance. Tropical montane rainforests are amongst the most diverse terrestrial communities, but also perhaps one of the most (sensitive and) susceptible to global warming projections. In the Australian Wet Tropics, the evolutionary history of rainforests has generally resulted in cool, wet upland adapted biota. Extensive field-based community surveys, comparative molecular datasets and paleo-distribution models each contribute independent lines of evidence to our current understanding regarding the historical sensitivity of these rainforest species to past climate-induced habitat fluctuations. Based upon observations of current environmental niche breadth, correlative models of future distributions in endemic vertebrates now raise concerns about the viability of populations (and species) for many low-dispersal habitat specialists. Ancient refugial areas of the highest conservation value are expected to fragment and contract significantly under even modest warming scenarios, and steep elevational gradients subdividing these historical refugia should face even stronger impacts. Several alternative scenarios of proposed warming (+1 to +7C) all previously resulted in significant reductions to core habitat size (40%-100%). Here we extend species distribution modeling to test the predicted effects of climate change on gene diversity in rainforest vertebrates for which comparative mtDNA phylogeographic data is available, taking into account ~80% of the total endemic stream frog (n=5) and lizard (n=12) species. Spatial responses in future warming models are summarised as reductions in the total number and/or range sizes of historical lineages per species. We contrast the role of paleo-environments in generating current diversity with the expected erosion of future diversity due to global warming, and discuss predicted losses of gene diversity in terms of both evolutionary heritage and future adaptive potential.