Because of their high dispersal abilities, birds are expected to manifest marked genetic structuring only at relatively large geographic scales. However, it is not well known how factors like nest site fidelity in a largely resident species could limit gene flow and increase genetic structuring in birds. In this study we use RAPD markers to estimate genetic structuring in a strongly sedentary species of the American tropics, the Russet crowned Motmot (Momotus mexicanus), within a tropical dry forest in central Mexico. Genetic structuring was assessed among 3 populations separated by a mean distance of only 25 km. We report that 12.9% of the total genetic variation is explained by differences among sites, which is quite high for a bird at this geographic scale. We propose that high nest site fidelity, brought on by a scarcity of suitable nest substrates, may be responsible for high genetic structuring in this species.