Fish populations of nine Ethiopian freshwater lakes were quantitatively sampled with a standardized protocol, using multi-mesh gill nets. In total, 27 species were identified, but only 14 species were common. Based on the common species, the fish communities showed large differences in their species composition, except for Lake Abaya and Lake Chamo which were similar. Most fish species were observed in only one or two lakes. Compared with the information reported in literature the present study generally underestimated the species richness. The empirical model of Amarasinghe and Welcomme (2002) for African lakes was used to estimate fish species richness, which was compared with species presence reported in literature. Biodiversity in the two northern highland lakes is low, but not lower than the model estimate. Lake Tana has a high biodiversity which is close to what is estimated by the model, but three Rift Valley lakes have low biodiversity, lower than estimated by the model. There are also strong indications for the Rift Valley lakes that species richness was higher in the past because the species richness reported in the older literature was generally much higher than those observed by us in the present study and those reported in the more recent literature. Threats like overfishing, high sediment load and degradation of habitats were identified. It is recommended that Ethiopia should develop guidelines for fishery legislation and implement it through an enforcement agency. Moreover, catchments management should be practiced to save the water bodies and their fish communities.