Siberian hamsters born into short daylengths near the end of the breeding season are reproductively inhibited from birth and delay gonadal maturation until the following spring. This vernal transition to a reproductive phenotype coincides with an abrupt increase in body weight, and both processes are triggered by an interval timing mechanism that becomes insensitive, or refractory, to short-day inhibition. It was previously demonstrated that hamsters born into simulated natural photoperiods in early August became photorefractory at later ages than hamsters born into September photoperiods. As a consequence of flexibility in the duration programmed by the interval timer, development of seasonal birth cohorts was synchronous with respect to the calendar date simulated by laboratory photoperiod. In the present study, hamsters were born into simulated August or September photoperiods. Hamsters from each cohort were given removable constant release melatonin implants to reversibly obscure the neuroendocrine representation of daylength between 3 and 9 weeks or 9-15 weeks of age. When control hamsters were given beeswax capsules throughout, August-born males were approximately 6 weeks older than September males at the onset of photorefractoriness as assessed by accelerated increases in body weight and testicular size. Females exhibited the same pattern in body weight. These measures were synchronized with respect to calendar date. Synchronization of cohorts was disrupted by melatonin capsules from 3-9 weeks of age but not by later implants. Melatonin implants altered synchronization by influencing the developmental trajectory of September-born hamsters without influencing the August cohort. These results demonstrate that the function of the interval timer underlying photorefractoriness is influenced by photoperiod and by melatonin. The endogenous pattern of melatonin signals adjusts the duration measured by the interval timer to insure that developmental milestones of seasonal cohorts are synchronized with environmental conditions.