Trichomycterus crassicaudatus is described as a new species from the Rio Iguaçu basin in southern Brazil. The new species has an exceptionally deep posterior region of the body (caudal peduncle depth 22.8–25.4% SL), resulting in an overall shape which distinguishes it at once from all other members of the Trichomycteridae. The caudal fin of the species is broad-based and forked, a shape also distinguishing it from all other species in the family. A number of autapomorphic modifications of T. crassicaudatus are associated with the deepening of the caudal region, including an elongation of the hemal and neural spines of the vertebrae at the middle of the caudal peduncle. Phylogenetic relationships of the new species are yet unresolved, but it shares a similar color pattern and a thickening of caudal-fin procurrent rays with T. stawiarski, a poorly-known species also from the Rio Iguaçu basin. Coloration and body shape also include similarities with T. lewi from Venezuela.