Remote and normally unpolluted high mountain lakes provide habitats with no or very limited anthropogenic influences and, therefore, their hydrodynamics are mostly regulated by the natural conditions. Researches in high mountain lakes deal with measuring and modeling the response of the habitats to environmental changes especially correlated to acid deposition, pollutants influx and climatic variability. The microbial world has also become a focus in many studies of these extreme ecosystems. Despite the pressure of harsh and extreme conditions, microbial communities living in these habitats developed flexible strategies and show quick adaptation to climate oscillation. New aspects in microbiological studies in recent high mountain lake research are presented in this paper.