Recent developments in the study of pain in animals have demonstrated the potential for pain perception in a variety of wholly aquatic species such as molluscs, crustaceans and fish. This allows us to gain insight into how the ecological pressures and differential life history of living in a watery medium can yield novel data that inform the comparative physiology and evolution of pain. Nociception is the simple detection of potentially painful stimuli usually accompanied by a reflex withdrawal response, and nociceptors have been found in aquatic invertebrates such as the sea slug Aplysia. It would seem adaptive to have a warning system that allows animals to avoid lifethreatening injury, yet debate does still continue over the capacity for non-mammalian species to experience the discomfort or suffering that is a key component of pain rather than a nociceptive reflex. Contemporary studies over the last 10 years have demonstrated that bony fish possess nociceptors that are similar to those in mammals; that they demonstrate pain-related changes in physiology and behaviour that are reduced by painkillers; that they exhibit higher brain activity when painfully stimulated; and that pain is more important than showing fear or anti-predator behaviour in bony fish. The neurophysiological basis of nociception or pain in fish is demonstrably similar to that in mammals. Pain perception in invertebrates is more controversial as they lack the vertebrate brain, yet recent research evidence confirms that there are behavioural changes in response to potentially painful events. This review will assess the field of pain perception in aquatic species, focusing on fish and selected invertebrate groups to interpret how research findings can inform our understanding of the physiology and evolution of pain. Further, if we accept these animals may be capable of experiencing the negative experience of pain, then the wider implications of human use of these animals should be considered.