Ostrom proposed the underpinnings of a framework for the systematic study of the governance of complex social–ecological systems. Here we hypothesize that Ostrom’s social–ecological system framework can be useful to build a classification system for small-scale benthic fisheries, regarding their governance processes and outcomes. The purpose of this paper is to contribute to knowledge accumulation of benthic fisheries. To tailor the framework, we relied on discussions among experts and a systematic literature review of benthic fisheries from 1980 to 2010. This literature review helped us refine variable definitions and provide readers with illustrative reference papers. We then illustrate the approach and its potential contributions through two studies of the emergence of self-organization in Mexico and Chile. We highlight synthetic lessons from the cases and the overall approach as well as reflect on remaining challenges to the development of a social–ecological system framework as a diagnostic tool for knowledge accumulation and synthesis.