The Balcones Escarpment of South-central Texas is a rolling landscape of Cretaceous carbonates where stratal continuity was complicated by more than 350 meters of Miocene displacement along the coincident Balcones Fault Zone. Faulting initiated the development of a coastward-evolving karst system, the current stage of which is represented by the modern Edwards Aquifer, located along the southeastern margin of the fault escarpment. Caves, springs and canyons along the aquifer outcrop provide habitat for more than 25 federally listed endangered species including terrestrial troglobites that occur only within vadose zone caves in the rapidly urbanizing San Antonio outskirts. The degree of connectivity between adjacent cave systems, and associated terrestrial troglobite habitats, is poorly understood, but has important implications for the evolutionary history, potential range, and management and conservation of endangered karst biota. The phylogeography of cave spiders of the Genus Cicurina shows a statistically significant correlation between genetic variability and structural components of the Balcones Fault Zone including the San Antonio Relay Ramp and the Culebra Anticline. MtDNA may provide a method of obtaining relative dates for cave entrance formation.