The karst area of the northeastern state of Goiás comprises two main municipalities: São Domingos and Posse. São Domingos is inside the limits of a Full Protection Conservation Unit known as Parque Estadual de Terra Ronca (PETeR), where a high number of caves occurs, some of them surpassing 10 km in length. Despite their protection by law, uncontrolled tourism has been threatening the integrity of the unique and fragile cave systems of São Domingos. On the other hand, the caves of Posse are much less visited, with its subterranean fauna poorly unknown and are strongly threatened by the urban areas and mining activities in the vicinity. We conducted six systematic surveys of invertebrates in 12 caves, seven of which are located in São Domingos and five in Posse, between 2010 and 2012. Immediately outside the caves, we sampled several microhabitats for comparison. We estimated richness, abundance, and taxonomic distinctness of the communities. We recorded 1,941 individuals of 344 morphospecies. Caves from São Domingos showed a higher species richness and were more taxonomic distinct than caves from Posse. Most morphospecies were considered troglophiles (188). We also found one trogloxene and one troglobite, as well as nine troglomorphic taxa that possibly are troglobitic as well. Both regions have markedly singular caves regarding its subterranean fauna, with high values of taxonomic distinctness. However, the richer caves were not necessarily the most taxonomic distinct. Conservation measures are especially necessary in the region of Posse, where caves are not legally protected and are within an area of significant urbanization. Cave entrances of Posse are near deforested vicinities, in some cases with domestic wastes and cement plants nearby.