The Benguela upwelling system is one of the most productive marine ecosystems in the world; however, little is known about the community structure of mesopelagic fishes in its northern (nBUS) and southern (sBUS) subsystems. We analyzed around 1900 specimens from 13 stations in 2019, austral summer, in the nBUS and 11 stations in the sBUS during the austral summer and found 88 species and 24 families of mesopelagic fishes. Seven distinct assemblages characterized by water mass, oxygen concentration in the surface layer, and chlorophyll concentrations between 50 and 100 m were identified. In 2021 in austral winter, 15 stations were analyzed, of which 7 belonged to sBUS and 8 to nBUS.