Abstract Background Many animals in coral reefs exhibit lunar cycles in their reproduction, showing synchronous gametogenesis and spawning at a particular moon phase. How these lunar reproductive cycles are endogenously regulated remains unknown, although changes in moonlight between the new moon and full moon are likely involved in this rhythmic event. Results This study evaluated the possible role of cryptochrome (cry1, cry2, cry3) in phase shifting and setting in the honeycomb grouper Epinephelus merra, which is a typical lunar spawner with full moon preference. qPCR analysis revealed that when fish were reared under alternating light-dark conditions, the transcript levels of cry1 and cry2, but not of cry3, in the diencephalon and pituitary gland showed daily variations. Weekly collection at midnight showed increases in the transcript levels of cry1 and cry2 in the diencephalon, but not the pituitary gland, from the first quarter moon through the last quarter moon. In comparison to the new moon, these transcript levels were significantly lower at all other sampling times. The artificial full moon conditions for 1 month resulted in increased cry transcript levels in both tissues at 2 (cry1) or 2 and 4 (cry2) weeks after the initiation of full moon conditions. Conclusions These results indicate the importance of transient changes in “brightness at night” in the response to moonlight for the phase shift and of “darkness at night” during the new moon for the phase set to the determined moon phase. We concluded that the moon phase-dependent oscillation of clock genes plays a role in lunar cycle-dependent behaviors in fish.