African Great Lakes (AGLs) contribute 2.7 million tonnes (~25%) to global inland fisheries production (11.9 mt) annually. This is composed of large species (> 20 cm total length, TL) and small pelagic species (< 20 cm, TL). At the turn of the 20th century, fisheries of the AGLs were dominated by large species (tilapine cichlids, Lates spp, cat fishes, Mormyrids, etc.) and management concentrated on these species. Overexploitation, habitat degradation, invasive species, pollution and climate change have contributed to a shift in composition and abundance, leading to dominance of small pelagic species such as haplochromines cichlids, sardines, clupeids, cyprinids (Neobola, Brycinus and Rastrineobola) and a few resilient large species. This research project presents trends in species composition, annual catches and biomass estimates to illustrate how small pelagic species have increased in contribution to overtake large fishes. In Lake Tanganyika, Stolothrissa tanganicae and Limnothrisa miodon contribute >50% to total catch by weight and the latter, contributes >75% to catches in Lake Kivu. Haplochromine cichlids contribute >60% to fish biomass in Lakes Malawi and Edward. R. argentea and resurging haplochromines contribute >70% to biomass and >60% to catches in Lake Victoria. Neobola and Brycinus species contribute >80% to catches in Lake Albert. It is only in the remote and lightly exploited Lake Turkana where 86% of the catch is by large species, showing that the AGLs have been taken over by small pelagic species. Management efforts should therefore target these emerging small pelagic and resilient large species.