Migratory birds can be efficient dispersers of pathogens, yet we know little about the effect of migration and season on the microbial community in avian plumage. This is the first study to describe and compare the microbial plumage community of adult and juvenile migratory birds during the annual cycle and compare the plumage community of migrants to that of resident birds at both neotropical and nearctic locations. We used length heterogeneity PCR (16S rRNA) to describe the microbial assemblage sampled from the plumage of 66 birds in two age classes and from 16 soil samples. Resident birds differed significantly in plumage microbial community composition from migrants (R > or = 0.238, P < 0.01). Nearctic resident birds had higher plumage microbial diversity than nearctic migrants (R = 0.402, P < 0.01). Plumage microbial composition differed significantly between fall premigratory and either breeding (R > or = 0.161, P < 0.05) or nonbreeding stages (R = 0.267, P < 0.01). Six bacterial operational taxonomic units contributed most to the dissimilarities found in this assay. Soil microbial community composition was significantly different from all samples of plumage microbial communities (R > or = 0.700, P < 0.01). The plumage microbial community varies in relation to migration strategy and stage of the annual cycle. We suggest that plumage microbial acquisition begins in the first year at natal breeding locations and reaches equilibrium at the neotropical wintering sites. These data lead us to conclude that migration and season play an important role in the dynamics of the microbial community in avian plumage and may reflect patterns of pathogen dispersal by birds.