Individual identification of small sized fishes such as the endangered delta smelt Hypomesus transpacificus remains a pressing need. We evaluated the stability of chromatophores as potential natural marks for subadult and adult delta smelt under low and high ambient light. We conducted three photo sessions of the dorsal head area at about three month intervals from fall 2014 to spring 2015. Image recognition was performed using visual tests (naked eye) and automated image recognition (TinEye's Match Engine). The stability of chromatophores between sessions was independently evaluated using: 1) the percent of correct matching (matching success), 2) similarity indices between matched images (match quality), and 3) the change in their relative size (chromatophore expression). Matching success (mean ± SD) was higher for visual tests (86 ± 12%) than automated tests (44 ± 30%), and was consistently higher from winter to spring for both visual (100%) and automated tests (80 ± 16%). Unlike visual tests, automated matching success differed between light treatments from winter to spring, and automated match quality was higher under low ambient light. Chromatophore expression increased between fall and winter, and decreased between winter and spring in both genders. Ambient light was less influential on matching success than ontogenetic changes between the subadult and adult stages. These results suggest chromatophores of delta smelt are more stable and have higher potential for practical use of natural marks under a wide range of ambient light scenarios when the adult stage is reached.