A new genus and two new species of Chelodesmidae are described from two caves of the João Rodrigues river system in Bahia state, northeastern Brazil: Strongylosomides troglobius sp. nov. and Rotundotergum elevatum gen. nov., sp. nov. The former species differs from congeners primarily by the gonopods showing the prefemoral process strongly fused caudally along its basal half to the acropodite and, in showing such troglomorphic traits as a nearly unpigmented and fragile body with thin tegument, it seems the first troglobiont to be documented in the genus. Moreover, this new species seems to be so remarkably similar to Leptodesmus stercoriarius Schubart, 1956, from Minas Gerais state, that the following new combination is warranted: Strongylosomides stercoriarius (Schubart, 1956), comb. nov. ex Leptodesmus de Saussure, 1859. The new genus, Rotundotergum gen. nov., seems to be especially similar to Eucampesmella Schubart, 1955, but differs clearly by the absence of a secondary process on the gonopodal prefemoral process, coupled with the latter being unusually long and strongly separated from the acropodite. The type species R. elevatum sp. nov., being partly clearly pigmented, seems to be only troglophilic. The region generally supports a typical dry tropical climate, whereas the caves represent sites with high humidity, this being essential for the survival of these and other species. However, these habitats remain unprotected by Brazilian law, while the João Rodrigues River system is threatened by irrigation projects, potential limestone exploitation, asphalt and road widening or construction that pass across the system and can collapse the rock, and pollution of the subterranean drainage. We hope that the new species described here could help us protect their type localities and the João Rodrigues River system as a whole.