Agroforestry has been widely practiced by Indonesian community since centuries ago. Nevertheless intensive research in agroforestry was only started in the last three decades. It can be understood if agroforestry has not yet been adopted in mainstreaming forestry and agriculture development in Indonesia. This paper aims to report the National Strategy on Agroforestry Research in Indonesia for the next two decades. The strategy was prepared by the team of authors following several phases, which include: a) review of research status of agroforestry, b) focus group discussions to involve team of experts and related stakeholders in formulating research topic priorities and implementation strategies; c) dissemination of the strategy concept to wider stakeholders to obtain feedbacks, and d) launching of the national strategy in front of wide stakeholders that include representatives from research institutes, universities, government agencies, nongovernmental organizations, and other related parties. The National Strategy of Agroforestry Research is proposing four priority research topics that will be the major research agenda in the field of agroforestry in Indonesia over the next two decades. These four priority topics are: 1) Smallholder production systems and markets of agroforestry practices; 2) Community based forest management on state forest areas; 3) Harmonization of agroforestry practices with global climate change, and 4) Enhancing agroforestry practices for environmental services. In addition to these priority research topics, the national strategy also describes the implementation strategy of the mentioned priority research topics.