The recent progress in deep learning has given rise to a non-invasive and effective approach for animal biometrics. These modern techniques allow researchers to track animal individuals on a large-scale image database. Typical approaches are suited to a closed-set recognition problem, which is to identify images of known objects only. However, such approaches are not scalable because they mis-classify images of unknown objects. To recognize the images of unknown objects as ‘unknown’, a framework should be able to deal with the open set recognition scenario. This paper proposes a fully automatic, vision-based identification framework capable of recognizing shark individuals including those that are unknown. The framework first detects and extracts the shark from the original image. After that, we develop a deep network to transform the extracted image to an embedding vector in latent space. The proposed network consists of the Visual Geometry Group-UNet (VGG-UNet) and a modified Visual Geometry Group-16 (VGG-16) network. The VGG-UNet is utilized to detect shark bodies, and the modified VGG-16 is used to learn embeddings of shark individuals. For the recognition task, our framework learns a decision boundary using a one-class support vector machine (OSVM) for each shark included in the training phase using a few embedding vectors belonging to them, then it determines whether a new shark image is recognized as belonging to a known shark individual. Our proposed network can recognize shark individuals with high accuracy and can effectively deal with the open set recognition problem with shark images.