The zooplankton assemblages in southern Chilean Patagonia are characterized by calanoid dominance and low species number that is observable under oligotrophic status and wide conductivity values, whereas at mesotrophic status the daphnids are dominant with high species number, and finally at hyper-saline environments halophilic species such as Artemia persimilis and/or the calanoid Boeckella poopensis predominate. In the present study data of different lakes and ponds between 45-53A degrees S were analyzed, with the aim to determine potential structures at different sites. For this purpose a null model based in guild structure was applied, considering each guild a different kind of water body (lake, small lake, permanent pond, ephemeral pond, and saline lake). The results revealed in two simulations that guild are structured. These results are similar with other descriptions on the basis of null models that revealed a random pattern of species associations for similar ecosystems due to many species repeated in all or practically all studied sites or similarities of ecological features. Ecological and biogeographical topics were discussed.