During the past 40 years many new techniques have emerged that have been pivotal in furthering understanding of the physiology of fish behaviour. Behavioural studies have been enhanced by video recording systems and software for computerized event recording analysis, fine scale anatomical studies by fluorescence confocal microscopy, neurophysiological studies by visualisation and neuroendocrinology with techniques for identifying, localizing and quantifying many neurochemicals within the central nervous system. This array of approaches has been complemented by developments in molecular biology that include the ability to monitor expression profiles for known genes in specific neural structures and within the whole transcriptome. This article explores how the deployment of new techniques during the last four decades has advanced the understanding of two extensively studied systems. The first of these is the fast-start escape response, concentrating on work on goldfish Carassius auratus and zebrafish Danio rerio. The second is the link between social experience and neuroendocrinology and how this relates to life-history traits in the cichlid Burton's mouthbrooder Astatotilapia burtoni. These two case studies are then used to explore the extent to which the behaviour of animals can be explained in terms of underlying physiological mechanisms.