Abstract: Lateolabrax maculatus is an important economic fish in China. Its reproduction is regulated by photoperiod. In this study, seven important clock genes (Bmal2, Npas4, Per2, Cry1, Cry1a, Cry2 and Timeless) were detected in the pituitary and hypothalamus of L. maculatus under three photoperiod conditions (16L∶8D, 8L∶16D and 12L∶12D). The results show that under 12L∶12D condition, Per2, Cry1, Cry2, Cry1a and Timeless displayed daily rhythmic expression in pituitary, and Per2, Cry2, Cry1 and Timeless displayed daily rhythmic expression in hypothalamus. The circadian rhythms of the same gene in pituitary and hypothalamus were also different. Long day (16L∶8D) or short day (8L∶16D) could change the amplitude of circadian rhythm and the peak phase, and some genes lost circadian rhythms under this condition.