The lack of knowledge about freshwater biodiversity in remote areas like montane Andean rivers is noticeable and hinder the development of efficient conservation plans for aquatic ecosystems. Habitat requirements of tropical Andean fishes have been poorly analysed, despite the relevance of these ecological features on the fish conservation strategies. The present study aimed to examine fish assemblages along the altitudinal gradient in tropical Andean rivers and their relationship to habitat features to detect the most relevant abiotic factors and their implication on conservation. This study was conducted on a regional scale, along six basins located in tropical Andes (500 to 2,692 m a.s.l.). We studied fish diversity and distribution and their habitats along these elevation gradients. We found 6,320 specimens from 53 genera. Our analysis for the six most common and widely distributed genera (Astroblepus, Brycon, Bryconamericus, Chaetostoma, Pimelodella and Trichomycterus) underlines the relevance of hydromorphological variables on fish community structure in the Andean montane rivers, whereas human alterations seem to be less significant. These findings could be useful for current management and conservation strategies considering present threats over tropical montane rivers.