This paper is derived from the experience of foresight project conducted by the Indonesian Institute of Sciences (LIPI) to determine research priorities in the marine sector based on sustainable blue economy. More than 80 marine experts from LIPI, governments, universities, NGO and other research organizations are involved in the project. The project used various foresight methods such as expert panels, questionnaire surveys, SWOT, STEEP analysis and scientometrics. Some core science issues and the gap analysis between the research that has been undertaken and relevant future research have been prepared based on Indonesian factual phenomena related to sustainable blue economy. The project identified six key issues and challenges faced by Indonesian marine sector in realizing sustainable blue economy in the next 15 years, (1) food security, (2) energy security, (3) marine pollution, (4) biodiversity, (5) sustainable coastal environment, (6) climate change. The results of this project show that topic related exploration of biomaterials from the sea, especially deep sea, and marine biotechnology by utilizing marine biota such as microalgae, seaweed, and sea cucumber are important research issues in responding to the blue economy developme