Marine microbiomes represent 90% of the total living marine biomass but only a small fraction of them can be cultivated. For this reason, they are an underexplored source of bioactive compounds, carbohydrate polymers and proteins, among others. Sampling the marine biodiversity, screening, identifying and isolating the relevant microbes is cumbersome, expensive and results in a heavy environmental burden, low yields, high costs and long times to market. Therefore, new approaches are necessary to overcome the limitations for the study of marine microbial communities and their “econological use”. BLUETOOLS will unravel the potential of marine microbiomes for healthier oceans and the Blue Bioeconomy through integration of different fields to develop cutting-edge tools that support fast, efficient AND sustainable exploration and exploitation of microbiomes, avoiding the drawbacks of conventional biodiscovery practices. The expected results of BLUETOOLS include discovering several hundreds of enzymes, rhodopsins, resistance genes, antimicrobials and anti-microfouling agents, thanks to a hybrid workflow of in silico and microfluidics-based functional discovery, resulting in the commercialization ≥400 enzymes for biocatalysis and ≥2 new solutions for plastic/polymer degradation, increasing the revenue of our industrial partners by 10-15%. BLUETOOLS assembles 5 leading European companies, 8 academic teams and 1 private RTO that have pioneered approaches in functional metagenomics, microfluidics, microbial ecology and synthetic biology. The presence of diverse, complementary industrial stakeholders in the consortium (from pharma to materials science to sustainability) at different stages in the research-to-market process (from RTOs to SMEs to large end-users) provides a unique opportunity for broad value creation. The planned activities will span 48 months and the project is estimated at ca. 9 M€, with 60% of the total dedicated to creating highly-qualified jobs