This paper examines how value chain coordination affects the ability of aquaculture producers to engage in eco-certification. Through a comparison of global salmon and shrimp value chains, it is argued that production risks and producer capacity are key determinants in the type of chain coordination adopted by lead firms. The results challenge global value chain governance theory by indicating that it is hierarchical (or vertically integrated) forms of coordination that are associated with high capabilities and low risk rather than market forms of coordination. It is also shown that eco-certification is more likely to be adopted in value chains with more engaged forms of coordination. This in turn means that eco-certification is a far less 'hands off' form of regulation than widely thought. The paper concludes that for certification to engage producers operating under market forms of chain coordination new arrangements are needed that can respond to challenges of improving producer capability and production risk. Statement of relevance: By understanding the role of risk and producer capability this paper contributes to improving the application and impact of eco-certification in global aquaculture production.