Here we explore a case study of endangered karst invertebrates in central Texas that considered evolution, genetic diversity, and climate change. During the course of climatic changes (e.g., glaciations) two million to ten thousand years ago, karst invertebrates retreated into the stable cave environments, while their respective surface relatives either emigrated or became extinct. Subsequent changes to subsurface habitats, e.g., fragmentation and isolation due to erosion or faulting, led to speciation among these species. By considering these barriers and species distribution, we developed recovery units and a strategy that should protect genetic diversity and conserve adaptive capabilities of these species in perpetuity. We are also beginning to consider climate change and how it is likely to affect these species and what we can do to prepare for this global threat on a local scale.