Terrestrial animals in subterranean habitats are often classified according to their degree of morphological or ecological specialization to the subterranean environment. The commonly held view is that, as distance into a cave increases, the frequency of morphologically specialized, i.e., troglomorphic, species or ecological specialization will increase. We tested this hypothesis for the fauna in 54 caves in Slovenia–the classical land for subterranean biology. We found that there exist two ecologically well separated terrestrial subsurface faunas: one shallow and one deep. 1) The shallow subterranean fauna, adapted to the terrestrial shallow subterranean habitats (SSHs) in the upper 10 m of subsurface strata, is most diverse. It consists of randomly distributed non-troglobionts and a major group of troglobionts adapted to the soil root zone. 2) The deep subterranean fauna is represented by a minor group of troglobionts, adapted to caves. Troglobionts are strictly divided between the two faunas. There is strong evidence that in karstic ecosystems with deep-rooted vegetation this might be a global pattern, or that in these locations only the shallow subterranean fauna exist.