Deeper knowledge about how species and communities respond to climate change and environmental gradients should be supported by evidence from the past, especially as modern responses are influenced by anthropogenic pressures, including human population growth, habitat destruction and fragmentation, and intensifying land use. There have been great advances in modeling species’ geographic distributions over shallow time, where consideration of evolutionary change is likely less important due to shorter time for evolution and speciation to occur. Over these shallow time periods, we have more resources for paleoclimate interpretation across large geographic landscapes. We can also gain insight into species and community changes by studying deep records of temporal changes. However, modeling species geographic distributions in deep time remains challenging, because for many species there is sparse coverage of spatial and temporal occurrences and there are fewer paleoclimate general circulation models (GCMs) to help interpret the geographic distribution of climate availability. In addition, at deeper time periods, it is essential to consider evolutionary change within lineages of species. I will discuss a framework that integrates evolutionary information in the form of phylogenetic relatedness from clades of extant closely related species, where and when there are associated fossil occurrences, and the geographic distribution of paleoclimate in deep time to infer species past geographic response to climate change and to estimate where and when there were hotspots of ancient diversification. More work is needed to better understand the evolution of physiological tolerances and how physiological tolerances relate to the climate space in which species occur.