Large, long-lived lakes, such as Lake Baikal and the African Great Lakes are known for their diverse endemic faunas. Nearby smaller isolated lakes have long been hypothesised to facilitate allopatric speciation, such as Lake Nabugabo at the edge of Lake Victoria, helping seed the radiation in the large lakes. Furthermore, crater lakes, formed by volcanic activity are often deep, long-lived and relatively isolated, and often host a number of closely-related endemics, becoming model systems for testing theories of sympatric speciation and adaptive radiation, such as Lakes Barombi Mbo in Cameroon, and Apoyo in Nicaragua. Here we report on studies of 9 crater lakes in southern Tanzania: Lakes Ikapu, Ilamba, Itamba, Itende, Kingiri, Kyungululu, Masoko (=Kisiba), Ndwati and Ngozi, plus the shallow satellite lakes Chikukutu and Chilingali in central Malawi. Additional notes are presented about fish species present in nearby river systems. The lakes differ considerably in surface area, depth and water chemistry. No permanently aquatic animals were observed in Lake Ngozi, the largest of the lakes, nor in Lake Ndwati. All of the other 7 craters lakes were found to contain cichlid fishes, comprising a total of 29 populations of which 24 are considered likely to be native, many meriting recognition as distinct species. At least one lake (Masoko) contains a diverging pair of cichlid ecomorphs likely to be undergoing sympatric ecological speciation. Another case might be the dwarf and large ecomorphs of Rhamphochromis in Lake Kingiri. In addition, 4 crater lakes are reported to contain members of other fish families: Clariidae, Cyprinidae, Danionidae and Procatopodidae. The lakes also hosted a variety of macro-invertebrates, including crabs, bivalves and gastropods. There is evidence of repeated attempts to stock all of these lakes with non-native fish species, in at least one case leading to the establishment of breeding populations of two species. This represents a major threat to these unique ecosystems. In Malawi, Lakes Chilingali and Chikukutu were recently joined as a result of damming of the outflow of the former. This ‘large Chilingali’ hosted a diverse fish fauna, including two apparently endemic haplochromine cichlid fishes of the genera Lethrinops and Rhamphochromis. The lake was heavily fished and attempts had been made to stock cages for tilapia culture using non-native populations of species already present in the lake. However, the dam was allowed to erode and it finally collapsed in 2011-13, resulting in the restoration of the previous condition of two inter-connected lakes. Little is known of the pre-impoundment lakes, but post-collapse, the lakes became shallow and swampy, with apparently greatly reduced fish diversity. Neither endemic species could be found when the lakes were sampled in 2016. Our work has indicated that the satellite lakes of Lake Malawi are important reservoirs of biodiversity that can play a major role in our understanding of speciation and adaptive radiation, but they are fragile systems currently threatened by poor management practices including intentional stocking of non-native fish.