Worldwide there is an increasing realisation that there is an inextricable link between the natural and human systems, and there is a need to integrate these into the governance of small-scale fisheries. The critical importance of adopting such an approach is argued in this paper by exploring the challenge of resource over-exploitation in the abalone fishery in South Africa and the loco fishery in Chile, both of which faced unsuccessful fishery closures and the implementation of Territorial Use Rights in Fisheries (TURFs). By exploring similarities and differences in fisheries context and approaches, these case studies highlight that although management strategies have been progressive on paper, they are compromised, to different degrees, by a lack of understanding of the socio-economic and political factors that are influencing the fisheries system. We argue that unless a more integrated approach is adopted to understand the social-ecological system as a whole, few long-term benefits will be secured for both the resources and the livelihoods of fishers.