An important characteristic for the persistence of social-ecological systems (SESs) over time is the adaptation of local institutions to the dynamic of the resources on which they depend, especially when communities face resources with high spatial and temporal variability. Previous studies on Territorial User Rights for Fisheries (TURF) in Chile (Áreas de Manejo y Explotación de Recursos Bentónicos, AMERB) showed that resources with high levels of variability, such as the highly valuable surf clam Mesodesma donacium, can have negative impacts on collective efforts among fishers to govern marine resources under AMERB, resulting in the collapse of local institutions in this boom-and-bust fishery. Here, we reflect on the only known case in Chile (Coquimbo Bay) in which local institutions, its governance mechanisms, and the surf clam M. donacium fishery have persisted over long periods of time, despite disturbances from the natural and social systems. Using participatory techniques, we draw on local fishers' in-depth knowledge of both the resource and their own historical coping mechanisms to understand the potential sources of institutional persistence among local fishers faced with a resource that has high levels of variability. We find that this unique success of a surf clam AMERB in Chile is attributed to the local conditions, such as the roots that fishers have to their village, the support by women and family, and also to the ecological settings of Coquimbo Bay and resource characteristics, that facilitate larval dispersal among the different bays, maintaining recruitment and production that sustains the AMERB. Thus, the persistence of the institution has been built over generations of coping with major disturbances to the SES, directly related to the persistence of M. donacium stocks over time, which has allowed the development of a well-structured institution with a strong fishers' organization, good leaders, a division of labor among members, shared responsibilities, and equitable income distribution.