Some marine microorganisms produce pathogenic compounds which cause diseases in tropical seaweeds used in aquaculture. On the other hand, some microorganisms are probiotics enhancing the healthy growth of macroalgae or produce relevant biochemical products and bioactive compounds with a considerable value for the pharmaceutical or chemical industry. The Aqua-Weed project investigates: (1) Basic and applied research of microbial communities: composition and functionality; (2) Identification of potential pathogens, probiotics and bacteria of biotechnological interest producing bioactive compounds; (3) Isolation of secondary metabolites to test their properties; (4) Assessment of management strategies; (5) Main issues and solutions. The benefits of the research are: (A) Baseline on the microbial diversity and functionality from marine macroalgae of Vietnam; (B) Sustainable management of tropical seaweed aquaculture; (C) Increment on the economic benefits and new algae-based products.