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Research-for-development (R4D), as a mode of foreign aid, is a practical way to support developing countries. However, few studies have assessed the scientific impacts of R4D projects. Here, we applied an integrated assessment approach to evaluate the scientific impact of research projects commissioned by the Australian Centre for International Agricultural Research's Fisheries Program in the Asia-Pacific region between 2000 and 2012. We use publication metrics and expert panel reviews to examine trends in scientific outputs among 73 fisheries and aquaculture research projects. Among projects, there was considerable variation in publication types and outputs (including academic papers, magazine articles, policy reports, books, and book chapters), and projects produced, on average, 10 publications at a funded-dollar cost of AU$41,000 per publication. Bilateral and multilateral projects tended to produce more refereed journal articles and citations per funded dollar than single-country projects, and publication outputs were poor for certain countries. With the exception of fisheries projects, larger (more highly funded) projects did not produce more journal articles per funded dollar than smaller projects. Project duration had no significant effect on the number of refereed publications, citation rates, or total citations per funded dollar across projects. Aquaculture projects had greater publication impact, per funded dollar than fisheries projects. Beyond the bibliometric measures, qualitative findings indicated that scientific impact was strongly influenced by motivations of project leaders and their institutions. We identified disparate impact performance among industries and countries. These findings could inform future overseas aid investments, policies and strategies. This study offers useful benchmarks for gauging scientific impacts of R4D programs and shows the value of using approaches that go beyond bibliometric measures.