Thin layers of water running over rocky surfaces are characteristic of madicolous habitats, which harbor a peculiar Chironomidae community. However, information on the identity, distribution, and ecology of madicolous chironomids in the Neotropical region are still sparse. The main purpose of this research is to reveal and contribute to the ecology of madicolous Chironomidae species, especially regarding their altitudinal distribution in the Atlantic Forest. Sampling was performed using our own designed emergence traps deployed from 0 to 2700 m a.s.l. in 70 sites in three mountains in southeastern Brazil. Sixty taxa of chironomids were collected and identified, of which only 22 are known to science. Most of the species showed a wider distribution than previously known, both in terms of geographic and altitudinal ranges, while others showed significant association with particular altitudinal bands (as evidenced by the indicator species analysis). Atlantic Forest mountainous regions are known to harbor one of the richest fauna in the world and have been suffering from several types of environmental impacts, including climate change, which will especially affect taxa living in specialized habitats. The narrow range of tolerance to environmental conditions verified for mountain species, and the fact that many of them are rare and endemic, make the conservation efforts in these areas indispensable.