The theory of island biogeography predicts the effects of habitat isolation and size on species richness, community assembly, and the persistence of species. Various studies showed that habitat conditions and the ecology of species are also of relevance in explaining community assembly. Geographically isolated habitats like caves with rather constant environmental conditions provide models to test for the relevance of the above described variables. In this study we analysed springtails living in karst caves of the Romanian Carpathians and Dobrogea region. We considered phylogenetic relatedness, habitat and species characteristics to identify the relevant drivers of community assembly. Our data show that species richness of single caves is low. Neither phylogenetic relatedness nor habitat filtering and competitive interactions seem to shape species composition or to affect species richness. We found that glacial-interglacial cycles with subsequent range contractions and expansions might have led to independent and multiple colonisations of caves. Furthermore, single caves might have acted as refugia and thus might have provided the prerequisite for distinct evolution processes, leading to a high level of endemicity of these animal species.