Traditional tagging methods for fishes can have issues relating to both animal welfare and economic costs. Biometric data such as iris patterns can be captured via digital cameras, which allows for non-invasive tagging and inexpensive and rapid analysis. The purpose of this study was to investigate if the iris of Atlantic Salmon (Salmo salar) is a suitable biometric template for long-term identification of individuals. Atlantic Salmon were individually tagged in the body cavity using PIT tags at the juvenile pre-smolt stage, and the left eye was photographed six times over a 533-day period. Changes in iris stability were assessed both qualitatively and using iris-recognition software. Identification of individual Atlantic Salmon using the iris was not successful over the entire period, as the iris pattern changed significantly with time. Over a shorter time period (four months) with frequent samplings, iris software was able to correctly identify individual fish. The results show that iris identification has potential to replace other methods for Atlantic Salmon over short timeframes.