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The Chilean fairy shrimp species are represented by the Branchinecta genus, which are poorly described, and mainly occur in shallow ephemeral pools in the Atacama Desert of northern Chile and the Southern Chilean Patagonian plains. The aim of the present study was to perform an initial ecological characterization of Branchinecta habitats and its associated communities in the Chilean Southern Patagonian plains (45-53 degrees S) using null models (co-occurrence, niche sharing and size overlap). The results of the co-occurrence analysis revealed that the species’ associations are structured, meaning that at different kinds of Branchinecta habitats, the associated species are different. I did not find niche sharing, which means interspecific competition is absent. Finally the size overlap analysis revealed structured patterns, which are probably due to environmental homogeneity or colonization extinction processes. The habitats studied are shallow ephemeral pools, with extreme environmental conditions, where continuous local colonization and extinction processes probably occur, which would explain the marked Branchinecta species endemism.