Caves may offer suitable refugia for troglophilic invertebrates during periods of unfavourable climatic conditions because of their stable microclimates. As a consequence, allopatric divergence from their epigean counterparts may occur, leading to formation of truly hypogean communities (the Climatic Relict Hypothesis). Unlike the well-studied effects of Pleistocene glaciations, we know little about how ancient climate changes drove the development of cave-dwelling organisms living at both middle and lower latitudes. We investigate the evolutionary history of the troglophilic spider genus Nesticella (Araneae, Nesticidae) in relation to Asian Neogene (23–2.6 Ma) climatic changes. Our analyses discern clear differences in the evolution of the two main clades of Nesticella, which occur in temperate/subtropical and tropical latitudes. Eastern Asian Nesticella gradually evolved greater sedentariness and a strict subterranean lifestyle starting from the middle Miocene Epoch (~15–14 Ma) in conjunction with the progressive deterioration of the climate and vegetational shifts. Caves appear to have acted as refugia because of their internally uniform temperature and humidity, which allowed these spiders to survive increasing external seasonality and habitat loss. In contrast, a uniform accumulation of lineages, long-lasting times for dispersals and the lack of a comparable habitat shifting characterised the tropical lineage. This difference in pattern likely owes to the mild effects of climate change at low latitudes and the consequent lack of strong climatic drivers in tropical environments. Thus, the mid-Miocene climatic shift appears to be the major evolutionary force shaping the ecological differences between Asian troglophilic invertebrates and the driver of the permanent hypogean communities in middle latitudes.