The importance of aquaculture in the fishery sector is increasing. The growth of aquaculture complements the stagnant growth of extractive fisheries. Many countries are now entering this emerging economic activity. This positive feature has some serious drawbacks when the country has no local institutions to ensure the environmental sustainability of aquaculture. The Chilean salmon farming industry has grown dramatically since the mid-1980s to become the leading exporter of farmed salmon after Norway. The sector, however, suffered decline due to the sanitary crisis in 2007. It is said that this crisis was caused by overexploitation and overconcentration of fish farms. This paper tries to explain the mechanisms of the sanitary crisis - a tragedy of the commons' - by paying attention to the role of endogenous factors such as local knowledge, capacity building, local ecological conditions and the emergence of local institutions, focusing on the case of salmon farming in Chile.