Differences in personality (within-individual consistency in behaviours across multiple contexts) are a widespread phenomenon across the animal kingdom. Variation in some personality traits has been previously linked to polymorphisms in the Serotonin transporter gene (SERT), associated with anxiety and risk avoidance. Zebrafish (Danio rerio) are shoaling fish, so prolonged isolation from conspecifics can cause them stress. Chronic stress may cause changes in individuals’ expression of behavioural syndromes; for example, previous research has found higher levels of anxiety in zebrafish after three weeks of individual housing. Accordingly, we explored the effects of social isolation on anxiety in zebrafish. We have undertaken a long-term behavioural repeatability experiment and shown anxiety levels of individual zebrafish, measured as the proportion of time spent in the bottom half of a novel tank over ten minutes, to be significantly repeatable over five weeks. Thus, we used this measure to phenotype zebrafish as anxious or non-anxious. Fish were then either kept individually or in groups for three weeks before reassessing anxiety levels, to determine whether individual housing changed anxiety levels, and whether any changes seen were dependent on initial levels of anxiety. We then examined whether individual variation in anxiety is linked to a genetic polymorphism, by sequencing regions of the SERT genes of the anxious and non-anxious fish. This research will help to refine our understanding of the effects of social isolation on anxiety, as well as identifying a potential genetic basis for these differences in zebrafish and other shoaling fishes.