Like most other insects, Drosophila visual system is sensitive to the spectrum of light from ultraviolet to green but is insensitive to red light. The circadian rhythms of Drosophila, however, can be entrained by red light through unknown mechanisms. Here, we discovered the corresponding organ and photopigments responsible for the circadian entrainment of Drosophila to red light from light emitting diode. The entrainment was eliminated by the loss of photic input from compound eyes using eya(2) or norpA(p24). We also found that the double Rhodopsin 1 (ninaE) and Rhodopsin mutant was not entrained to red light. These results indicate that Drosophila can entrain the circadian rhythm to red light through Rhodopsin 1 and Rhodopsin 6 in compound eyes.