In mammals, adult neurogenesis is a restricted phenomenon, taking place in only two distinct areas of the brain, the subventricular zones and the hippocampus. The rate of adult neurogenesis can be regulated through a multitude of factors, including drugs, hormones, environmental complexity, learning and stress. Social stress is a particularly strong negative modulator of adult hippocampal neurogenesis, an effect that may be mediated through glucocorticoid activity. The neurogenic rate may in turn influence memory learning and mood. Teleost fish have a considerably higher rate of adult neurogenesis, with proliferative zones located in all parts of the brain. Its regulation is, however, still poorly understood. A recent study demonstrates that cell proliferation in ranbow trout telencephalon is down-regulated in socially stressed individuals. In the current study, quantitative real-time PCR is used to investigate the effect of social stress on the expression of three genes related to neurogenesis in different parts of the rainbow trout brain. These are the proliferation marker PCNA, the neuronal differentiation factor NeuroD and BDNF, which is involved in stimulation of neurogenesis, survival of new neurons and synaptogenesis. Our results indicate that social stress in not solely a negative modulator of neurogenesis. We found that expression of NeuroD is up-regulated in hypothalamus of socially subordinate rainbow trout, compared to dominant individuals and controls. This indicates that a rise in neurogenic rate in hypothalamus is caused by social stress experienced by subordinate individuals. Other brain parts exhibited a contrasting pattern, with enhanced PCNA expression in small fish regardless of treatment in the cerebellum and optic tectum. In view of the possible U-shaped dose response and/or time response relationship between stress and brain structural plasticity, a more detailed time-course study is called for to determine the exact effect of chronic stress on the process of neurogenesis in rainbow trout.