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In this study, we analyse the distribution and species richness of epibenthic and planktonic Cladocera (Crustacea: Branchiopoda) in 62 Uganda crater lakes, spread across the climatic gradient between the sub-humid shoulder and semi-arid floor of the East African Rift Valley. Together, these lakes cover large environmental gradients in salinity, trophic conditions and depth. In total, 36 species of Cladocera were encountered in the freshwater lakes (<1,500 mu S/cm), whereas only a single species was found in the true saline lakes (>10,000 mu S/cm). Cladoceran species richness in individual lakes was found to be determined primarily by the presence of a well-developed littoral belt of submerged and emergent aquatic macrophytes, pH and salinity. The highest species richness occurred in fresh but eutrophic shallow waters, with relatively low pH (6.5-7) and dense aquatic macrophyte growth. As identified by multivariate statistical analysis, the distribution of Cladocera species among the Uganda lakes was most strongly determined by nutrient availability (measured as total phosphorus), the presence and diversity of aquatic macrophyte habitat, pH, mean annual temperature and the fraction of the crater catchment that is currently under agriculture. Since Cladocera play an important role in aquatic food webs, and as such contribute to the ecological integrity of aquatic ecosystems, an increased understanding of the environmental controls underlying their distribution provides valuable information on aquatic ecosystem functioning needed for management and conservation. The significant turnover of cladoceran species composition along the sampled environmental gradients demonstrates their potential as biological indicators for water quality and ecosystem health in East African lakes. Our results suggest that changes in land use are the greatest threat to natural ecosystem functioning in these African lakes, and particularly so in the shallower lakes.