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Non-vagile taxa such as terrestrial molluscs are susceptible to stochastic environmental events that can cause local extinctions or population declines, and extinctions of terrestrial mollusc species are among the highest documented. Many terrestrial snails are habitat specialists, and genetic studies using both allozyme and DNA sequence data have indicated that many species contain substantial and geographically structured genetic variation. In this study, we assess the genetic variation within two species of the rare terrestrial snail genus Prestonella, an inhabitant of rocky areas along water courses in the southern Great Escarpment of South Africa, and correlate genetic diversity to climatic variables. DNA sequence data from mitochondrial 16S rDNA and partial cytochrome oxidase I genes indicate that neither species is monophyletic, and that populations are deeply divergent, even over distances of a few hundred metres. Principal components anaylsis of climatic variables derived from two databases indicates that genetic diversity of the populations is correlated to moisture-related climatic variables. Populations with little or no diversity occur in more arid regions, and are thus most at risk from any future climatic changes that would increase aridification. These moisture variables are thus potent drivers of genetic bottlenecks and may have resulted in historical climate filtering or limitation of the distribution of these species. Temperature appears to be a less important variable, a finding supported by physiological data based on heart rates that show that death occurs only at temperatures far higher than found in their environment.