AbstractCircannual rhythms often rely on endogenous seasonal photoperiodic timers involving ‘clock’ genes and Clock gene polymorphism has been associated to variation in phenology in some bird species. In the long-distance migratory barn swallow Hirundo rustica, individuals bearing the rare Clock allele with the largest number of C-terminal polyglutamine repeats found in this species (Q₈) show a delayed reproduction and moult later. We explored the association between Clock polymorphism and migration scheduling, as gauged by light-level geolocators, in two barn swallow populations (Switzerland; Po Plain, Italy). Genetic polymorphism was low: 91% of the 64 individuals tracked year-round were Q₇/Q₇ homozygotes. We compared the phenology of the rare genotypes with the phenotypic distribution of Q₇/Q₇ homozygotes within each population. In Switzerland, compared to Q₇/Q₇, two Q₆/Q₇ males departed earlier from the wintering grounds and arrived earlier to their colony in spring, while a single Q₇/Q₈ female was delayed for both phenophases. On the other hand, in the Po Plain, three Q₆/Q₇ individuals had a similar phenology compared to Q₇/Q₇. The Swiss data are suggestive for a role of genetic polymorphism at a candidate phenological gene in shaping migration traits and support the idea that Clock polymorphism underlies phenological variation in birds.