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Behavioural phenotypes are under many influences from external and internal environments. The extent to which genetics affects behaviour has been a focus of recent study. Gradually, evidence demonstrating the influences of genes upon behaviour has mounted in a wide range of studies from family resemblance to gene knockouts to microarrays. A major challenge in behavioural ecology is to investigate the genomic architecture of behaviour, including the numbers, locations and effects of genes associated with behaviour, with the aim of understanding how complex behaviours are influenced by genetic variation. A recent transition in the study of animal behaviour has been in the interest of studying those behaviours that are correlated. When behaviours are correlated, there may be underlying genetic correlations that act as a constraint from performing the most optimal behaviour for the situation. Three traits that are often associated are aggression, boldness and stress responsiveness and it is useful to study these together and separately in order to establish whether genetic correlations exist. Stress, and the related behaviours aggression and boldness, have a significant bearing on the welfare of rainbow trout in aquaculture and are important when considering breeding programmes and rearing conditions for fish farming. These studies aimed to assess the genomic complexity of the evolutionarily important traits, stress responsiveness, aggression and boldness, including the genomic links between behaviours, so as to provide empirical evidence for underlying mechanisms of behavioural syndromes. In addition, this study aimed to identify candidate genes associated with stress and aggression using novel genomic techniques. A combination of genomic approaches was used to understand genomic components of animal behaviour, under the wider context of a behavioural syndrome, where behaviours are correlated across context. The association between heterozygosity and stress responsiveness and the related behaviours was tested to determine genomic influences on behaviour. The number and genomic locations of regions associated with stress responsiveness were determined to understand the level of complexity associated with stress. Using next generation sequencing, the transcriptomes of aggressive and less aggressive fish were characterised, with the aim of identifying the numbers of genes associated with aggressiveness. Crucially, novel candidates for the study of individual and correlated behaviours were identified. Moreover, candidate genes were studied in relation to both stress responsiveness and aggressive behaviour. The results showed that genetic diversity was linked with aggression but not stress responsiveness or boldness. Moreover, genome-wide heterozygosity, rather than heterozygosity at single loci, appeared to be associated with aggressiveness. Similarly, genome regions potentially associated with stress responsiveness were located across the genome. Genomic control of behaviour was complex, where many genes were associated with aggressive behaviour and these effects may interact with the effects of other genes. Furthermore, I showed that novel applications of techniques can yield novel candidates for behaviour, where I identified genome regions that are potentially associated with stress responsiveness and candidate genes associated with aggression using a transcriptome, including unidentified sequences. These results highlighted the complex mechanisms that regulate apparently correlated behaviours. To further the study of behavioural genomics, the impact of environmental conditions and previous experience to investigate non-genomic effects should be considered. Moreover, there may be regulatory systems and pathways that interact both at the genetic and environmental level, which may be studied with the use of next generational genomic tools. These findings may be relevant for better understanding the effects of stress and the related behaviours aggression and boldness in rainbow trout in aquaculture. By determining novel candidates for these traits, it may be possible to use these as biomarkers for the early detection of negative effects or to aid marker-assisted breeding programs.