The zooplankton assemblages in deep, mostly oligotrophic northern Patagonian lakes are characterized by a low species number and a marked dominance of calanoid copepods, as well as often by the presence of large mixotrophic ciliates (Stentor). In the present study, data collected in field work on four northern Patagonian lakes were analysed using co-occurrence of null models, with the aim to determine potential regulating factors for the observed crustacean and mixotrophic ciliate assemblages, using a presence-absence matrix. The null model uses species co-occurrence, and the basis of this model is that the species associations observed are random. The results revealed the absence of regulating factors and indicate that the sites are relatively homogeneous, with low species numbers, and similar plankton assemblages at all study sites. This finding coincides with similar descriptions for zooplankton assemblages in other Chilean Patagonian lakes. © 2011 BRILL.