The ocean is an important ecosystem, and aquatic animals play an important role in the biological world, especially in aquaculture. How to accurately and intelligently recognise and detect aquatic animals is one of the urgent problems in the field of underwater biological detection. The wide applications of artificial intelligence (AI), especially deep learning (DL), provide new opportunities and challenges for the efficient and intelligent exploration of aquatic animals. DL has been widely used in the visual recognition and detection of terrestrial animals, but it is in the early stages of use for aquatic animals due to the complexity of underwater environment and the difficulty of data acquisition. Here, this article reviews the current application status of DL for aquatic animals, potential challenges and future directions. The key advances of DL algorithms applied to the visual recognition and detection of aquatic animals are generalised, including datasets, algorithms and performance. The applications of DL are summarised in aquatic animals, including image detection, video detection, species classification, biomass estimation, behaviour analysis and food safety. Furthermore, the challenges are summed up and classified in the object recognition and detection domain for aquatic animals. Finally, further research direction is discussed and the conclusions are drawn. The key advances of DL in the recognition and detection of aquatic animals will help to further excavate and extend the application of DL in the field of marine biological exploration.