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As a consequence of climate change and open net-pen salmon farming, wild Atlantic salmon Salmo salar are increasingly likely to encounter elevated temperatures and parasite abundances during their early marine migration. Such stressors can compromise fitness by diminishing liver energy stores and impairing cardiac muscle. To assess whether temperature and infestation by salmon lice Lepeophtheirus salmonis are important correlates of liver energy stores and cardiac muscle performance in juvenile salmon, we experimentally infested fish at 3 abundances of louse infestation (zero, low, and high) and 5 temperatures (10, 13, 16, 19, and 22°C). At the end of the experiment (i.e. when sea lice reached adulthood), we calculated the percent dry weight of the liver (%DWL; a proxy for liver energy stores) and cardiosomatic index (CSI; a proxy for cardiac muscle performance) of each fish and fitted 5 linear mixed-effects models to both of these responses. For both %DWL and CSI, the best-supported model included additive fixed effects for both infestation level and temperature. Our top models predicted that, relative to zero infestation, high infestation reduces %DWL by 5.7% (95% CI: 5.3-6.2%) and increases CSI by 15.9% (14.4-18.0%), and low infestation reduces %DWL by 2.6% (2.2-3.0%) and increases CSI by 7.8% (6.7-10.0%). Our work suggests that stressors associated with ocean warming and coastal salmon aquaculture can compromise wild salmon fitness through the impairment of vital organs. peerReviewed