I present a comparative analysis of the cave fauna composition for two karst areas in the Atlantic tropical rain forest: the extensively studied Ribeira Valley, southeastern Brazil, and the small and poorly known Rio Pardo region, southern Bahia state, northeastern Brazil. These regions also are compared to other Brazilian karst areas. The cave fauna from Rio Pardo appears to be more similar to the fauna of other tropical caves in the Caatinga and Cerrado domains than to the cave fauna of the subtropical Ribeira Valley. Ecological data, including probable trophic relationships, are presented, and special conservation problems related to karst areas, with examples from the Atlantic rain forest cave taxa, are discussed.