Since the spring of 2014, the mussel farming of Charente-Maritime and Vendée (French Atlantic coast) has experienced an unprecedented crisis. Mass mortality events of blue mussel (M. edulis) have affected livestock areas, decimating up to 100% of production in some farming areas. Investigation for infectious agents in moribund mussels revealed presence of bacteria capable of inducing mortalities. In this context, the MORBLEU research project (DPMA-Ifremer agreement) was initiated to explore potentially aggravating factors, associated or correlated with mortality of mussels. The aim of the present study is to support the hypothesis that these mortality episodes can be linked to an evolution of microbial communities. Based on historical data from Ifremer networks and specific monitoring (NGS metabarcoding) we put in prospect mortality events and evolution of phytoplankton and bacterial diversity. The holistic approach carried out in the MORBLEU project will contribute to describe potential links between dynamic equilibrium of the planktonic microbial communities and “health" of mussel livestocks.