The effects of light wavelength on photoperiodic clock were determined in the migratory male blackheaded bunting (Emberiza melanocephala). We constructed an action spectrum for photoperiodic induction (body fattening, gain in body mass, and gonadal recrudescence) by exposing birds for 4.5 weeks to 13 h light per day (L:D = 13:11 h) of white (control), blue (450 nm), or red (640 nm) color at irradiances ranging from 0.028 to 1.4 W m−2. The threshold light irradiance for photoinduction was about 10-fold higher for blue, compared to red and white light. Phase-dependent effects of light wavelength on the photoperiodic clock were further examined in the next two sets of skeleton photoperiods (SKPs). In the first set of SKPs, birds were exposed for four weeks to asymmetrical light periods (L:D:L:D = 6:6:1:11 h) at 0.25 ± 0.01 W m−2; two light periods applied were of the same (450 nm: blue:blue, B:B; 640 nm, red:red, R:R) or different (blue:red, B:R or red:blue, R:B) wavelengths, or of white:white (W:W, controls). Photoperiodic induction occurred under R:R and B:R, but not under B:B and R:B light conditions; the W:W condition induced an intermediate response. The second set of SKPs used symmetrical light periods (L:D:L:D = 1:11:1:11 h), and measured effects also on the activity rhythm. Birds were first exposed to one of the four SKPs (R:R, B:B, R:B, or B:R) for three weeks, subsequently were released into dim constant light (LLdim; ˜0.01 W m−2, the night light used in an L:D cycle) for two weeks, and then were returned to respective SKPs for another three weeks. Activity was greater in the R:R compared to B:B, and in B:R compared to R:B light condition. Zugunruhe (intense nighttime activity, indicating migratory restlessness in a caged situation) developed under the R:R and B:R, but not the B:B and R:B, light condition. Under LLdim, all birds free-ran with a period >24 h, the Zugunruhe had a circadian period longer than the daytime activity, and the re-entrainment to SKPs was influenced by the position of light periods relative to circadian phase of the activity rhythm. Photoperiodic induction at the end of 8 weeks was found in the R:R and B:R, but not in B:B, light conditions; in the R:B condition only one bird had initiated testes. Taken together, these results suggest that in the blackheaded bunting, the circadian photoperiodic clock is differentially responsive to light wavelengths; this responsiveness is phase-dependent, and the development of Zugunruhe reflects a true circadian function. Wavelength-dependent response of the photoperiodic clock could be part of an adaptive strategy in evolution of the seasonality in reproduction and migration among photoperiodic species under wild conditions.