Variations between distinct natural markings of freckled hawkfish (Paracirrhites forsteri) could allow in situ identification of individuals from underwater photography. Receiver operating characteristic analysis was used to assess the ability of the Interactive Individual Identification System (I3S) software to assist in discriminating between images of P. forsteri individuals. This study's results show the high discriminant ability of I3S to differentiate between unlike individuals and identify images of the same individual. The ability to use automatic computer‐aided assistance in the study of this species will enable future research to explore behaviour and movements of individuals in the wild.