Subterranean organisms always attracted the attention of humans using caves with various purposes, due to the strange appearance of several among them and life in an environment considered extreme. According to a classification based on the evolutionary and ecological relationships of these organisms with subterranean habitats, first proposed by Schiner in 1854 and emended by Racovitza in 1907, three categories have been recognized: troglobites, troglophles and trogloxenes. The Schiner-Racovitza system has been discussed, criticized, emended, the categories have been redefined, subdivided, original meanings have changed, but it is used until now. Herein we analyze in a conceptual framework the main ecological classifications of subterranean organisms, from Schiner to Trajano, in 2012, so far the last author to introduce a relevant conceptual change on the categories definitions, incorporating the source-sink population model. Conceptual inconsistencies are pointed, especially with regards to the generally ill-defined trogloxene category, and the correspondence between categories according to the original sense and in alternative classifications is discussed. Practical criteria for distinction between these categories and difficulties for their application are presented. The importance of rightly classifying subterranean populations according to the Schiner-Racovitza system for conservation of these fragile and mostly threatened habitats is discussed.