Chilean Patagonia has numerous unpolluted terrestrial and aquatic ecosystems, containing many unpolluted and pristine lakes and ponds. Published and unpublished information collected between 1989 and 1990 in lakes and ponds within Torres del Paine National Park, an unpolluted and pristine protected area in Southern Chile (51°S), was analysed in this study. A principal component analysis (PCA) was applied using mainly chemical parameters, zooplankton species richness and biomass. It was found that the cations (Ca, Na, Mg) chloride, seston and chlorophyll concentrations together with zooplankton biomass and zooplankton species richness were the main contributing variables to the derived model. According to this model, the following groups were observed: 1 st group-deep oligotrophic lakes with low zooplankton biomass and low species richness; 2 nd group -small mesotrophic lakes and ponds with moderate conductivity, zooplankton biomass and species richness. This latter group included small ponds with high nutrient and chlorophyll concentrations. A null model for species co-ocurrence was applied. The results in two of three simulations denoted that species associations are not random, which would agree with the PCA results. These results showed that oligotrophy and low ionic concentrations, and probably fish presence, are important regulatory factors in zooplankton community structure. These explain the similar patterns observed between Argentinean and Chilean Patagonian lakes.