Proponents of integrated, collaborative, and adaptive governance advocate the inclusion of a diversity of stakeholders and their knowledge and values in governance processes. This paper examines knowledge interactions at different scales of decision-making within two marine social-ecological systems in southern Kenya. Ecological knowledge systems are shown to be diverse and fluid even within broad conceptual classifications. Knowledge interactions at the local level are mediated by socio-cultural, institutional, and historical factors, whilst knowledge integration within district to national levels is primarily structured by institutional factors linked to centralised decision-making. In policy arenas, knowledge bounded to the marine environment is subjugated by knowledge dealing with terrestrial parks, inland fisheries, and wildlife tourism.