Even though the Chilean lakes are characterized by their oligotrophy, a transition from oligotrophy to mesotrophy, due human intervention, has been reported in some lakes. Nevertheless, there are still some pristine and unpolluted small lakes and ponds in mountain zones, free of human intervention and surrounded by native forests. Nine unpolluted, oligotrophic and pristine water bodies located in Cañi Park, a mountain zone with altitudes between 1000 to 1500 m a.s.l and forests where Nothofagus dombeyi, N. pumilio and Araucaria araucana predominate, were studied. For each sampled lake, zooplankton was collected and environmental parameters were obtained (conductivity, total dissolved solids, and chlorophyll concentration). A null model of species co-occurrence was applied to determine randomness in species associations. All sites revealed low species richness (< 6); the calanoid copepod Boeckella gracilis Daday, 1902 was present in all sites. The results of the null model indicated randomness or absence of regulatory factors in species associations. Only few species occur in practically all localities. Also, a significant inverse association between chlorophyll concentration with percentage of calanoid copepods and a weak direct association between chlorophyll concentration and percentages of cladocerans were found.