Monitoring social interactions between individuals in large, high-density groups poses several challenges. Here we demonstrate that relative concentrations of serotonin (5-Hydroxytryptamine, 5-HT) and its principal catabolite 5-Hydroxyindoleacetic acid (5-HIAA) in brain tissue of individual fish reflect social organisation in large groups of farmed Atlantic salmon. In the central nervous system of vertebrates, the monoamine neurotransmitter/neuromodulator 5-HT is critical for maintaining adaptive physiological, cognitive and emotional processes. In both teleost fish and mammals it has previously been shown that social interactions in small groups lead to elevated 5-HT release and/or metabolism in subordinate individuals, as indicated by the 5-HIAA/5-HT concentration ratio. In the current study, evidence is presented of non-linear dominance hierarchies in farmed Atlantic salmon (Salmo salar) kept at high rearing densities. The physiological effect of these hierarchies was decreased when food resources were abundant, although some subordinate fish still showed altered brain serotonergic activity and failed to grow even feed was available in excess. The largest effect of decreased feed rations was seen in fish of intermediate size, where competition appeared to increase with reduced access to feed. The largest individuals in each rearing unit showed low 5-HIAA/5-HT ratios independent of feeding regime. A novel observation, with respect to previous studies, was that elevated brain 5-HIAA/5-HT ratios resulted from decreased 5-HT concentrations rather than elevated 5-HIAA in small fish. Thus, in light of the serotonin deficit hypothesis of depression, it cannot be excluded that social stress is important for animal welfare even in large, relatively homogenous groups of animals reared in captivity.