By the terms set by international agreements for the conservation of Yukon River salmon, 2009 was a management success. It was a devastating year for many of the Alaska Native communities along the Yukon River, however, especially in up-river communities, where subsistence fishing was closed in order to meet international conservation goals for Chinook salmon. By the end of summer, the smokehouses and freezers of many Alaska Native families remained empty, and Alaska’s Governor Sean Parnell petitioned the US Federal Government to declare a fisheries disaster. This paper reviews the social and ecological dimensions of salmon management in 2009 in an effort to reconcile these differing views regarding success, and the apparently-competing goals of salmon conservation and food security. We report local observations of changes in the Chinook salmon fishery, as well as local descriptions of the impacts of fishing closures on the food system. Three categories of concern emerge from our interviews with rural Alaskan participants in the fishery and with federal and state agency managers: social and ecological impacts of closures; concerns regarding changes to spawning grounds; and a lack of confidence in current management methods and technologies. We show how a breakdown in observation of the Yukon River system undermines effective adaptive management and discuss how sector-based, species-by-species management undermines a goal of food security and contributes to the differential distribution of impacts for communities down and up river. We conclude with a discussion of the merits of a food system and ecosystem-based approach to management, and note existing jurisdictional and paradigmatic challenges to the implementation of such an approach in Alaska.