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Desert lakes are among the world's most threatened ecosystems, but they are clearly less studied when compared to lakes in more moist regions. The Badain Jaran desert is an exceptional desert due to the presence of numerous megadunes and over hundred small lakes which exhibit large variation in pH and salinity. These lakes have received surprisingly small attention in terms of aquatic ecology and only few biota groups have been studied so far. Here, we present results on the cladoceran communities based on the study of 40 lakes in the Badain Jaran desert. Surface sediment samples were analysed in order to obtain species inventories as complete as possible. Unsurprisingly, we found the most saline lakes devoid of cladocerans, but the subsaline lakes harbor few salt tolerant species. The most interesting finding is the ability of these species to thrive in highly alkaline conditions. The Badain Jaran desert lakes should be studied in more detail (e.g. complete zooplankton and phytoplankton inventories) in order to understand these interesting ecosystems. • 40 lakes were sampled for cladocerans using surface sediment samples. • Saline lakes were devoid of cladocerans, whereas in subsaline lakes cladocerans were detected. • The richest cladoceran communities were found in most alkaline lakes pH > 10. [ABSTRACT FROM AUTHOR]