Keywords: catfish; threatened species; mapping; habitatAbstract: Steindachneridion melanodermatum, an endemic and endangered species, is the largest catfish in the Lower Iguaçu River basin. Currently, the wild population of this species no longer exists in most of this basin, probably due to the loss of habitat by successive hydroelectric dams. This study evaluated the spatial distribution and abundance of S. melanodermatum in the last free-flowing river stretch of approximately 190 km downstream from the Salto Caxias Dam, upstream of the Iguaçu Falls, as well as some tributaries. Hydroacoustic and fishing campaigns were performed between September 2010 to December 2016 to characterize the preferred habitat. A total of 180 specimens was sampled with higher abundances in a protected area near Iguaçu Falls in the Iguaçu National Park. Twenty-four deep pools were identified with maximum depths ranging from 5 to 25 m: 21 pools were along the main channel of the Iguaçu River, and three pools were in tributaries. Deep pools are preferential habitats for this species, especially the deep pool called Poço Preto (P23) and its surroundings. Conservation strategies are required to protect these habitats and prevent S. melanodermatum from becoming extinct, such as establishing deep pools as ecological sanctuaries, intensifying the inspection of illegal fishing, and maintaining dam-free tributaries.