The lacustrine ecosystems located in the Andes Mountains in the Atacama desert and in the Chilean Southern Patagonia are characterized by their high levels of salinity, the zooplankton in these sites are characterized by a marked predominance of calanoid copepods at low or intermediate salinity levels, and at high salinity levels pratically only the genus Artemia is dominant. Data on levels of salinity and zooplanktonic composition in both regions were collected in field work and from published data. Statistical analysis showed a marked inverse association between salinity and species richness that was notoriously significant for Andes Mountains (R = -0.8193; p = 0.0037), whereas for Southern Patagonia there were observed weakly similar results, caused by lack of data between 5.0-15.0 g/l. Both zones observed calanoid dominance at low and moderate salinity levels between 3-51 g/l and 1-16 g/l for Andes Mountains and Southern Patagonia, respectively, and Artemia genus was dominant at salinities above 100 g/l for Andes Mountains and 20 g/l for Southern Patagonia. Ecological and biogeographic effects, and comparison with zooplankton assemblages of Australian saline lakes are discussed in the present study.