The ecosystem approach had been recognized as a platform for enhanced cooperation between regional seas organisations (RSOs) and regional fisheries bodies (RFBs). This paper will explore some of the opportunities and challenges for enhanced cooperation between RSOs and RFBs towards the achievement of relevant marine and coastal Aichi Biodiversity Targets and Sustainable Development Goals (SDGs) in a mutually supportive manner and in accordance with the ecosystem approach. To that end, the paper will explore how Parties to the Convention on Biological Diversity (CBD) can implement the guidelines and commitments they adopted on the ecosystem approach at the regional level, with a view to mainstreaming the conservation and sustainable use of biodiversity in the fisheries sector, and addressing synergies among relevant Aichi Biodiversity Targets and SDGs. This is particularly the case of Aichi Biodiversity Target 6 (sustainable fisheries), which expressly calls for the application of ecosystem based approaches in fisheries management; and with the implementation of ecosystem approaches being an indicator for SDG 14.2 (enhanced oceans resilience and productivity). By highlighting these synergies, natural linkages with, inter alia, SDGs 2.1 (ending hunger and malnutrition) and 1.5 (building resilience of the poor) will also be explored, and recommendations regarding integrative management tools will be provided.