The PyriSentinel project (pyrisentinel.eu) focuses on studying the microorganisms of high mountain lakes in the Pyrenees using advanced long-read DNA sequencing techniques. Approximately 300 lakes have been examined, each characterized by geographical isolation, extreme environmental conditions, and climatic variability, which contribute to their remarkable microbial diversity. Characterizing these planktonic communities is essential for understanding ecosystem productivity, as they play a key role in nutrient cycling, water purification, and interactions with macroorganisms, both at trophic levels and through their pathogenic potential. The lakes have been characterized by describing physico-chemical features and correlating those data with the microbial biodiversity. Biomonitoring serves as a crucial tool for assessing the health of these sentinel lakes. The project, involving experts from France, Spain, and Andorra, fosters international collaboration, consolidating knowledge and coordinating efforts while implementing innovative techniques for microbial sampling and analysis. PyriSentinel provides a comprehensive insight into the genetic diversity of aquatic microorganisms in the Pyrenees. By contributing to global microbiome characterization efforts, the project supports the development of effective monitoring strategies for these unique ecosystems, ensuring their conservation and sustainable management in the face of environmental change.