ABSTRACT The food base in the subterranean environment consists mainly of allochthonous materials. In this environment the resources are distributed generally in a heterogeneous dispersed way and the distribution of resources and their availability determine where the terrestrial invertebrates will reside, which is important for understanding ecological relationships and to establish conservation strategies. Thus, we tested how the complexity of substrates influences the richness and composition of the subterranean terrestrial invertebrates in the Presidente Olegário karst area, southeastern Brazil. We carried out collections in six caves during both dry and wet seasons, using combined collection methods. We observed different distributions in relation to the substrate, because the environmental heterogeneity increases the amount of available niches for the fauna. Some taxa showed a preference for specific substrates, probably related to the availability of food resources and humidity and to body size restriction, emphasizing the niche differentiation between species. Anthropogenic impacts can cause irreversible alterations in the subterranean fauna because the subterranean environment is dependent on the surface for input of trophic resources. On-going impacts in the Presidente Olegario karst area, like agriculture, pastures, gas extraction, and hydroelectric projects, are therefore a serious threat to subterranean biodiversity and this region should be prioritized for conservation.