The subterranean environment harbors species that are not capable of establishing populations in the epigean environment, i.e., the obligatory subterranean species. These organisms live in a unique selective regime in permanent darkness and usually low food availability, high air humidity in terrestrial habitats, and low temperature range allied to other unique conditions related to lithologies and past climatic influences. The pressure to increase Brazil's economic growth relies on agricultural/pastoral industries and exporting of raw materials such as iron, limestone, ethanol, soybean, cotton, and meat, as well as huge reservoir constructions to generate electricity. Mining (even on a small scale), agricultural expansion, and hydroelectric projects are extremely harmful to subterranean biodiversity, via the modification and even destruction of hypogean habitats. The Brazilian subterranean species were analyzed with respect to their distributions, presence on the IUCN Red List, and current and potential threats to hypogean habitats. A map and three lists are presented, one with the described obligatory subterranean species, one with undescribed taxa, and one with the current and potential threats to the hypogean environment. To date, 150 obligatory subterranean species have been recorded in Brazil, plus at least 156 undescribed troglomorphic taxa, totaling 306 Brazilian troglobites/obligatory cave fauna. We also analyzed the current and potential cave threats and the conservation actions that are underway to attempt to compensate for loss of these habitats. In according to the Brazilian legislation (Decree 6640) only caves of maximum relevance are fully protected. One strategy to protect the subterranean fauna of Brazil is the inclusion of these species in the IUCN Red List (one of attributes that determines maximum relevance for caves); however, one of the IUCN assumptions is that the taxa must be formally described. It is clear that the description and proposed protection of Brazilian subterranean biodiversity depends on more systematics studies.