Increasing public concern for the welfare of fish species that human beings use and exploit has highlighted the need for better understanding of the cognitive status of fish and of their ability to experience negative emotions such as pain and fear. Moreover, studying emotion and cognition in fish species broadens our scientific understanding of how emotion and cognition are represented in the central nervous system and what kind of role they play in the organization of behavior. For instance, on a (...) macro neuro-architecture level the brains of fish species look dramatically different from those of mammals, while such a dramatic difference does not (always) occur at the level of emotion- and cognition-related behavior. Here, therefore, we discuss the evidence of emotion and cognition in fish species related to underlying neuro-architecture and the role that emotion and cognition play in the organization of behavior. To do so we use a framework encompassing a number of steps allowing a systematic approach to these issues. Emotion and cognition confer on human and non-human animals the capacity to compliment and/or override immediate reflexes to stimuli and so allow a large degree of flexibility in behavior. Systematic research on behavior that in mammals is indicative of emotion and cognition has been conducted in only a few fish species. The data thus far indicate that in these species brain-behavior relationships are not fundamentally different from those observed in mammals. Furthermore, data from other studies show evidence that behavior patterns related to emotion and cognition vary between fish species as well within fish species, related to sex and life history stage for example. From a welfare perspective, knowledge of such variability will potentially help us to design optimal living conditions for fish species kept by humans. (shrink)