Light is a major external environmental factor that influences the circadian rhythm of photosynthetic organisms and various physiological phenomena, such as growth, maturation, and behavior. The number of light-reaching organisms changes depending on the season and atmospheric conditions, and the intensity and wavelength of light differ depending on the organisms inhabiting the environment. Altered light changes the circadian rhythm of fish, which is controlled by clock genes, such as period 2 (Per2), cryptochrome 1 (Cry1), and melatonin. In this study, we set the zeitgeber time (ZT; 14 light-10 dark, LD) based on the actual sunrise and sunset times and examined Per2 and Cry1 activities, levels of aralkylamine N-acetyltransferase (AANAT), and melatonin in Pholis nebulosa, a drifting seaweed species exposed to irregular light. Per2 and Cry1 levels increased during the daytime and decreased after sunset. The AANAT levels decreased during the daytime and increased during the night. Melatonin concentration was highest around midnight (ZT21, 23:30), but exhibited similar concentrations during the daytime. While the activity of Per2, Cry1, and AANAT levels exhibited a typical circadian rhythm observed in most vertebrates, melatonin concentrations did not show a significant difference between the daytime and nighttime. These findings provide insights into the circadian rhythm patterns of organisms exposed to irregular light environments, such as P. nebulosa, which differ from those of typical fish species.