Small-scale fisheries are subject to various governing institutions operating at different levels with different objectives. At the same time, small-scale fisheries increasingly form part of domestic and international market chains, with consequent effects for marine environments and livelihoods of the fishery-dependent. Yet there remains a need to better understand how small-scale fisheries market chains interact with the range of governance institutions that influence them. In this paper, we examine how multiple governance systems function along market chains, in order to identify opportunities for improved multiscale governance. We use three small-scale fisheries with varying local to global market chains operating in the Asia-Pacific region to develop a framework for analysis. Drawing from Interactive Governance theory we identify governing systems that have come to operate at particular sections in each market chain. We recognize four institutions that shape the governance over the length of the chain; namely those centred on (a) government, (b) private sector and pricing, (c) decentralized multistakeholder management and (d) culture and social relations. The framework shows how diverse arrangements of these governing institutions emerge and take effect along market chains. In doing so, we seek to move away from prescribed “ideals” of universal governing arrangements for fisheries and their market chains, and instead illuminate how governing systems function interactively across multiple scales.