Southwestern freshwater lakes of the Aquitaine coast host a unique aquatic plant diversity, which maintain vital ecosystem functions. However, anthropogenic activities and global change pose significant threats to these communities, leading to extinctions. We first aim to investigate the genetic diversity of nine macrophytes species composing isoetids communities from five lakes. To this end, we will study the genetic variation applying sequence-based nuclear microsatellite genotyping across 4000 sampled individuals. The distribution of genetic diversity within and between lakes will help understanding populationlevel processes as well as identifying ancient and contemporary factors structuring populations and communities. These results will provide insights into the adaptation capacity, demographic history, dispersal abilities and structure of macrophytes populations. In addition, we aimed to deepen our understanding of ecological process to a larger biological scale in examining the correlation between genetic and taxonomic diversity using the SGDC (species-gene diversity correlation) framework. This method aims to determine if the same ecological processes occur at different biological scales as well as to establish if taxonomic diversity can be a good proxy for genetic diversity. In essence, the aim of this project is to provide valuable information for conservation management plans in the Aquitaine region and to contribute to our understanding of how freshwater plant communities are structured and how they respond to threats. The ultimate goal of this project is to work with the stakeholders to ensure the conservation of these sensitive but fundamental populations.