Geographical isolation is the main speciation-inducing factor. The current biogeographical and phylogenetic patterns of various organisms, among them gastropods, reflect past speciation events promoted by isolation resulting from geological processes. This is especially the case in the east of the Mediterranean Basin, where large-scale geological events, coupled with climatic changes, created a high environmental and topographic heterogeneity. This article reviews and summarises the studies on relationships between the phylogeography of the Truncatelloidea (Caenogastropoda) and the major geological events which have shaped the geomorphology of the Eastern Mediterranean and the Balkans. The evidence suggests that the geological events having the greatest impact on the biogeography of the truncatelloideans were: the initiation (~12 Mya) and end (~10 Mya) of the Mid-Aegean Trench; the beginning (5.96 Mya) and end (i.e. Zanclean Flood, 5.33 Mya) of the Messinian Salinity Crisis, and climatic oscillations during the Pleistocene (2.58–0.0117 Mya), especially the glaciations. Isolation shapes the pattern of inter-population diversity especially in the cave and spring fauna. The results of studies on the evolution of truncatelloideans in isolated cave habitats are also presented.