This paper updates Recent Advances in the African Great Lakes: Fisheries, Biodiversity and Cichlid Evolution published by the Freshwater Biological Association in Freshwater Forum (Lowe-McConnell, 2003). Since 2003 many international teams have continued research on lakes Malawi, Victoria and Tanganyika. This review discusses the decline of the important commercial fisheries in all three lakes, together with changes in ecological and limnological conditions which the fishes now face. It also describes advances in our understanding of how the spectacular flocks of endemic cichlid species have evolved in each lake and continue to coexist.