The circadian system of the marine unicellular alga Gonyaulax polyedra consists of at least two separate circadian oscillators. One of these controls the rhythm of bioluminescence, the other the rhythm of swimming behaviour. These two oscillators have separate light input mechanisms. The bioluminescence oscillator responds mainly to blue light whereas the aggregation oscillator is also sensitive to red light. Therefore, one of the chlorophylls is a likely candidate for the light receptor of the aggregation oscillator. Owing to their differences in spectral sensitivity, the two oscillators can be internally desynchronized when frequent dark pulses (e.g., five minutes every 20 min) are given in otherwise constant red light. Single bright red light pulses interrupting a constant dim blue background shift the bioluminescence oscillator similarly to dark pulses. They also lead to aftereffects in the period of the bioluminescence rhythm, indicating that the aggregation oscillator has a different phase response to red light pulses. In contrast, blue light pulses interrupting a dim red background shift both oscillators in a similar way and do not significantly alter the circadian period following the light pulse. The mammalian phosphagen creatine shortens the period of the bioluminescence rhythm significantly in blue light but not in red. Because it also increases the sensitivity of the phase response of the bioluminescence oscillator, we propose that creatine acts on its blue-sensitive light input mechanism.