In mammals, the circadian clock in the suprachiasmatic nuclei (SCN) is mainly synchronized to photic cues provided by the daily light/dark cycle. Phase-shifts produced by light exposure during the night are correlated with rapid induction of two clock genes, Per1 and Per2, in the SCN. Nonphotic stimuli such as behavioral and pharmacological cues, when presented during the subjective day, induce behavioral phase-advances and a down-regulation of Per1 and Per2 expression in the SCN. When applied during the subjective day, dark pulses in continuous light also produce phase-advances. These phase-shifting effects have been interpreted as reflecting either a photic image mirror, nonphotic cues, or a combination of both. Here we evaluated in Syrian hamsters housed in constant light how dark pulses applied in late subjective day affect levels of Per1, Per2 and Cry1 mRNA. Four-hour dark pulses with no access to a wheel produced 1.2±0.4 h phase-advances of locomotor activity rhythm while control manipulation induced non-significant shifts (0.1±0.2 h). Dark pulses transiently down-regulated Per1 and Per2 mRNA levels in the SCN by 40 and 20% respectively, while the levels of Cry1 mRNA remained unaffected. In behaviorally split hamsters in which Per oscillations were asymmetric between the left and right sides of the SCN, dark pulses reduced Per expression in the half-SCN with high Per. This study shows that exposure during the late subjective day to dark pulses independent of wheel-running have nonphotic-like effects on the SCN clock at both behavioral and molecular levels.