Fish distribution in the Mono River is not well known. This river is interesting because of human influence, especially the Nangbéto hydroelectric dam built on it. In this study, fish communities in the Mono River between the middle (Atchinédji) and lower (Djonnougui) reaches were seasonally surveyed using two sets of gillnets of different mesh sizes (10, 12, 17, 20 and 22 mm mesh sizes) in 2012 and 2013 in ten sampling sites. In addition to fish harvesting, environmental variables were also quantified. According to fish assemblages, sampling site ordination was studied using the nonlinear clustering technique, the self-organizing map (SOM). An index of indicator value (IndVal) was calculated for each species to see if there is any indicator species, which could characterize the different types of communities identified by the SOM. A total of 37 species belonging to 28 genera and 19 families were recorded. The most widely distributed species were Brycinus cf. imberi, B. longipinnis, and B. macrolepidotus, which belong to the Alestidae family. Results from the SOM analysis indicate a three-cluster structure, mainly related to the location of the sampling sites. Our data run contrary to the ichthyofauna homogeneity trend in a river’s middle course, and this is probably due to a major human interference in the river like the construction of the Nangbéto dam. A significant correlation between species distribution and environmental variables was found. Distance from source, altitude, forest area, canopy height, water velocity, conductivity, transparency and pH are the most discriminating fish community parameters. The IndVal method identified several characteristic species in the typical assemblages identified by the SOM technique. We suggest for any human interventions in the river that special attention should be given to the protection of the diversity of fish habitats in order to conserve their associated species and therefore preserve the biodiversity of the ichthyofauna of the Mono River.