Abstract Natural marks can provide a noninvasive approach to identify individual fishes, such as the endangered Delta Smelt Hypomesus transpacificus. We evaluated the feasibility of chromatophores as natural marks in cultured adult Delta Smelt and used the dorsal view of the head, where chromatophores are particularly abundant. Digital images of the head were compared among three photo sessions conducted at nearly 6-week intervals in winter–spring 2013 (n = 292–234). Images were evaluated visually (naked eye) and by automated image recognition (TinEye Application Programming Interface [API]). Visual analysis enabled us to correctly identify all 60 fish examined between each pair of photo sessions. The TinEye API also correctly identified 100% of the individuals when it was able to, but the software did not identify 6–41% of the fish between photo sessions; the longer the period between photo sessions, the lower was the percentage of fish identified by the TinEye API. Fish exposure to outdoor ambient light constricted chromatophores, but the percentage of image matching was not influenced by ambient light, gender, or spawning condition. We conclude that it is feasible to identify individual adult Delta Smelt throughout the spawning season without having to tag them, but further development of automated image recognition is needed.