Diurnal vertical migration of the red-tide dinoflagellate Karenia mikimotoi and environmental conditions were measured in Hiroshima Bay and the Yatsushiro Sea in July of 2012 and 2015, respectively. The uppermost daytime depths for K. mikimotoi were 1.3–6.0 m and did not correspond to the pycnocline; most cells reached the bottom each night. Although the incident photosynthetic photon flux density (PPFD) varied among days, average PPFDs at the mean cell distribution depths were similar (59–65 µmol m−2 s−1) between compensation and saturation PPFDs for photosynthesis. Total daily PPFD at the mean depth was between the growth threshold and that for maximum growth rates. Among visible wavelengths, the photon flux density of green and yellow light (500–600 nm) at the mean depth was major (about 61% of the total), and the PFD of blue (400–500 nm) was always relatively minor (about 20%). Laboratory results identified green light as sufficient for K. mikimotoi growth, yielding growth rates equivalent to those under blue light. This study suggests that the vertical cell distribution depth during the daytime is regulated by underwater light transmission and that green light is valuable for growth and photosynthesis of K. mikimotoi.