“The Science We Need For The Ocean We Want.” We are on the threshold of a new and exciting era of discovery in the oceans that will shape the development of human endeavours for decades to come. New insights on the significance of the microscopic scale of ocean life has shown this level affects almost every aspect of our lives (health, food, industry, ecosystems). For society’s future, we need to investigate the science of marine microbiomes, integrate the novel technologies discovered and initiate policies that foster truly sustainable marine development. The United Nations will dedicate the next decade to Ocean Science for Sustainable Development. The Decade’s vision and mission are consistent with the objective of the Atlantic Ocean Research Alliance (AORA) between the European Union, Canada and the United States, that is to “advance the shared vision of an Atlantic Ocean that is healthy, resilient, safe, productive, understood and treasured, to promote the well-being, prosperity and security of the Atlantic for present and future generations”. Relevant to the missions of both AORA and the Decade, here, we outline how the marine microbiome is at the heart of the ocean as a living system, driving its nutrient and biogeochemical cycles, forming the basis of its food webs, performing essential and yet unknown functions in climate regulation, including buffering the effects of global change. Furthermore, the oceans are a largely untapped resource for biodiscovery and the bioeconomy, with a high potential for the development of new products and processes. To ensure early coordination and interoperability guided by a shared vision, we need to bring together science, industry and policy makers to advance the “Next Great Exploration of the Oceans”. The following Roadmap is the result of an international cooperative effort between the United States, Canada, and the European Union produced within the AORA framework and consistent with the Galway Statement on Atlantic Ocean Cooperation. Within the marine microbiome Roadmap, three thematic pillars have been identified by AORA scientists and policy makers, all supported with underlying cross-cutting elements: Environment and Climate, Food Value Chain and Biodiscovery.