Chilean Patagonia has protected mountainous areas with evergreen native forests; in which the lakes and rivers, of volcanic or glacial origin, are oligotrophic. In Bulgaria, there are mountainous zones with native forests and associated lakes of volcanic origin. The aim of the present study is to carry out a preliminary comparison of zooplanktonic crustaceans in lake ecosystems associated with native forests of Chilean Patagonia and of Bulgarian mountains. The study revealed that the lakes studied in Chilean Patagonia are associated mainly with Nothofagus forests; they are oligotrophic, with a low number of zooplanktonic crustacean species. Similar results were observed for Bulgarian mountain lakes associated with Fagus forests. A null model analysis of species co-occurrence was applied to the two groups of lakes, and the result revealed the absence of regulatory factors in species associations. These studies agree with similar descriptions of lakes in Andean Patagonia and New Zealand. They highlight the important role of native Nothofagus forests in Argentina and Chile, and of Fagus forests with associated soil properties in Bulgaria, in the oligotrophy of the lakes studied.