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High mountain lakes are extreme freshwater ecosystems and excellent sentinels of current global change. They are likely among the most comparable ecosystems across the world. The largest contrast occurs between lakes in temperate and tropical areas. The main difference arises from the seasonal patterns of heat exchange and the external loadings (carbon, phosphorus, metals). The consequence is a water column structure based on temperature, in temperate lakes, and oxygen, in tropical lakes. This essential difference implies that, in tropical lakes, one can expect a more sustained productivity throughout the year; a higher nutrient internal loading based on the mineralization of external organic matter; higher nitrification-denitrification potential related to the oxyclines; and a higher metal mobilization due to the permanently reduced bottom layer. Quantifying and linking these and other biogeochemical pathways to particular groups of organisms is in the current agenda of high-mountain limnology. The intrinsic difficulties of the taxonomic study of many of the organisms inhabiting these systems can be now overcome with the use of molecular techniques. These techniques will not only provide a much less ambiguous taxonomic knowledge of the microscopic world, but also will unveil new biogeochemical pathways that are difficult to measure chemically and will solve biogeographical puzzles of the distribution of some macroscopic organism, tracing the relationship with other areas. Daily variability and vertical gradients in the tropics are the main factors of phytoplankton species turnover in tropical lakes; whereas seasonality is the main driver in temperate communities. The study of phytoplankton in high-mountain lakes only makes sense in an integrated view of the microscopic ecosystem. A large part of the plankton biomass is in heterotrophic, and mixotrophic organisms and prokaryotes compete for dissolved resources with eukaryotic autotrophs. In fact, high-mountain lake systems are excellent model ecosystems for applying an investigation linking airshed to sediments functional views. Additionally, the study of the mountain lakes districts as functional metacommunity units may reveal key differences in the distribution of organisms of limited (slow) dispersal. We propose that limnological studies at tropical and temperate high mountain lakes should adhere to a common general paradigm. In which biogeochemical processes are framed by the airshed-to-sediment continuum concept and the biogeographical processes in the functional lake district concept. The solid understanding of the fundamental limnological processes will facilitate stronger contributions to the assessment of the impacts of the on-going global change in remote areas.