Hatchery rearing significantly influences the phenotypic development of fish, with potential adverse effects for the post-release performance of hatchery-reared individuals in natural environments, especially when targeted for stock enhancement. To assess the suitability of releasing hatchery-reared fish, a comprehensive understanding of the phenotypic effects of captive rearing, through comparisons with their wild conspecifics, is essential. In this study, we investigated the divergence in body coloration between wild and hatchery-reared marbled rockfish Sebastiscus marmoratus. We examined the selection preferences for different light colors and assessed the impact of different ambient light colors on the morphological color-changing ability of juvenile marbled rockfish. Our findings revealed significant differences in body color between wild and hatchery-reared marbled rockfish. The hue and saturation values of wild marbled rockfish were significantly higher than those of their hatchery-reared counterparts, indicative of deeper and more vibrant body coloration in the wild population. Following a ten-day rearing period under various light color environments, the color of wild marbled rockfish remained relatively unchanged. In contrast, hatchery-reared marbled rockfish tended to change their color, albeit not reaching wild-like coloration. Light color preference tests demonstrated that wild juvenile marbled rockfish exhibited a preference for a red-light environment, while hatchery-reared individuals showed a similar but weaker response. Both wild and hatchery-reared marbled rockfish displayed notable negative phototaxis in the presence of yellow and blue ambient light. These results highlight the impact of hatchery rearing conditions on the body color and morphological color-changing ability, and provide insight into light color selection preferences of marbled rockfish. To mitigate the divergence in phenotypic development and produce more wild-like fish for stocking purposes, modifications to the hatchery environment, such as the regulation of ambient light color, should be considered.