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Our human-dominant world can be viewed as being built up in two parts, social and ecological systems, each consisting of multi-level organizations that interact in a complex manner. However, there are knowledge gaps among those interactions. In this paper, we focus on studies filling two types of gaps in the socioecological system, some of which are case studies in the East Asia region and others are discussed in a more general context. First, we address the gaps between different levels of organizations in ecological systems, namely, (1) the importance of plant trait plasticity in bridging evolution and ecology, (2) linking primary producer diversity and the dynamics of blue carbon in coastal ecosystems in the Asia–Pacific region, and (3) research direction of climate change biology to fill the gaps across evolution, community, and ecosystem. Also included is (4) the gap between ecological monitoring programs and theories, which also addresses the potential of citizen science. Second, we illustrate the gaps between ecological and social systems through ongoing development of an ecosystem management framework, i.e., ecosystem-based disaster risk reduction. Finally, we summarize the benefits of filling the gaps for ecologists and society.