Abstract The present work brings information on threats to the subterranean fishes in Brazil. Currently, at least 36 species are known, 22 of which are already formally described. Endemism is the rule for most of them. Regarding their conservation, these fishes are in general considered threatened: and most of the already formally described species are included in national lists of threatened fauna, and only four of them are included in the global list of the IUCN. Regarding habitats, Brazilian subterranean fishes occur in alluvial sediments (part of the hyporheic zone), shallow base-level streams, flooded caves, lakes in the water table, upper vadose tributaries, and epikarst aquifers. We detected 11 main threats, mainly related to agriculture, pasture, and hydroelectric plans, but unmanaged tourism and pollution are also significant threats. Two threats affect a high number of species (physical change of the habitat and food restriction). The river basins with the higher number of identified threats are the upper Tocantins (eight) followed by the upper Paraguaçu (six). Effective proposals to protect this neglected component of the Brazilian biodiversity are still scarce, such as monitoring projects and their function in the subterranean communities, besides education projects aiming to develop public awareness.
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