Increased farm salmon production has heightened concerns about the association between disease on farm and wild fish. The controversy is particularly evident in the Broughton Archipelago of Western Canada, where a high prevalence of sea lice (ectoparasitic copepods) was first reported on juvenile wild pink salmon (Oncorhynchus gorbuscha) in 2001. Exposure to sea lice from farmed Atlantic salmon (Salmo salar) was thought to be the cause of the 97% population decline before these fish returned to spawn in 2002, although no diagnostic investigation was done to rule out other causes of mortality. To address the concern that sea lice from fish farms would cause population extinction of wild salmon, we analyzed 10-20 y of fish farm data and 60 y of pink salmon data. We show that the number of pink salmon returning to spawn in the fall predicts the number of female sea lice on farm fish the next spring, which, in turn, accounts for 98% of the annual variability in the prevalence of sea lice on outmigrating wild juvenile salmon. However, productivity of wild salmon is not negatively associated with either farm lice numbers or farm fish production, and all published field and laboratory data support the conclusion that something other than sea lice caused the population decline in 2002. We conclude that separating farm salmon from wild salmon-proposed through coordinated fallowing or closed containment-will not increase wild salmon productivity and that medical analysis can improve our understanding of complex issues related to aquaculture sustainability.B ecause salmon aquaculture production has rapidly increased over the past three decades, the potential for environmental impacts of salmon farms has generated heightened scientific and public interest (1, 2). One concern about salmon farms is that they are the source of ectoparasitic sea lice infestations that might reduce the marine survival of wild salmon (3, 4). In the Broughton Archipelago region of Western Canada (Fig. S1), farming of Atlantic salmon (Salmo salar) began in the late 1980s, and annual farm salmon production increased steadily to 17 Gg by 1999 (Fig. S2). Pink salmon (Oncorhynchus gorbuscha) is the most abundant wild salmon species in the Broughton Archipelago; they enter the marine environment at a very small size (0.2 g), and they return to natal streams to spawn 2 y after their parents (5). Because age at maturity never varies, they have distinct evenand odd-year populations ( Fig. S2 and SI Text). Record high numbers of pink salmon returned to spawn in rivers of the Broughton Archipelago in 2000 and 2001 (Dataset S1), but these returns were followed by population decline of 97% in 2002 and 88% in 2003 (Figs. S2 and S3 and SI Text). When juvenile pink salmon in the Broughton Archipelago were first examined for sea lice in June 2001, more than 90% were infested-leading to the hypothesis that sea lice from fish farms were the cause of population collapse in 2002 (4).Adult pink salmon are a natural host for the sea louse species Lepeophtheirus salmoni...