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In deserts, pond cladocerans suffer harsh conditions like low and erratic rainfall, high evaporation, and highly variable salinity, and they have limited species richness. The limited species can take advantage of ephippia or resting eggs for being dispersed with winds in such habitats. Thus, environmental selection is assumed to play a major role in community assembly, especially at a fine spatial scale. Located in Inner Mongolia, the Ulan Buh desert has plenty of temporary water bodies and a few permanent lakes filled by groundwater. To determine species diversity and the role of environmental selection in community assembly in such a harsh environment, we sampled 37 sand ponds in June 2012. Fourteen species of Cladocera were found in total, including six pelagic species, eight littoral species, and two benthic species. These cladocerans were mainly temperate and cosmopolitan fauna. Our classification and regression tree model showed that conductivity, dissolved oxygen, and pH were the main factors correlated with species richness in the sand ponds. Spatial analysis using a PCNM model demonstrated a broad-scale spatial structure in the cladoceran communities. Conductivity was the most significant environmental variable explaining cladoceran community variation. Two species, Moina cf. brachiata and Ceriodaphnia reticulata occurred commonly, with an overlap at intermediate conductivity. Our results, therefore, support that environmental selection plays a major role in structuring cladoceran communities in deserts. [ABSTRACT FROM AUTHOR]