Hypermelanosis of the blind side of Japanese flounder frequently occurs in post-metamorphic juveniles reared in hatcheries. Due to the morphological similarity between darkened blind-side skin and normal ocular-side skin, hypermelanosis is regarded as a transition from normal blind-side skin to that of the ocular side. Hypermelanosis appears only in rearing tanks without sand on the bottom, and its incidence tends to increase under stressful conditions; however, the specific mechanisms responsible for its occurrence have not been identified to date. In teleosts, the hypothalamus-pituitary-interrenal axis (HPI axis) is activated under stress, which then accelerates cortisol secretion. Therefore, in this study, we orally administered cortisol to Japanese flounder to examine its effect on hypermelanosis. The results of our study indicated that cortisol promoted hypermelanosis in a dose-dependent manner. In addition, the effect of cortisol was canceled out in juveniles reared in tanks with bottom sand, suggesting that the well-documented inhibitory effect of bottom sand is stronger than the stimulatory effect of cortisol (i.e., stress) on hypermelanosis. However, administration of the cortisol antagonist RU486 failed to inhibit hypermelanosis, suggesting the contribution of other stimulatory factors to this process. Therefore, our findings strongly suggest that stress-induced cortisol release has the adverse effect of promoting hypermelanosis in juvenile flounders reared without bottom sand.