Effects of vertebrate-associated microbiota on physiology and health are of significant interest in current biological research. Previous studies have focused on host-microbiota interactions in captive-bred mammalian models. These interactions and their outcomes are still relatively understudied, however, in wild populations and non-mammalian taxa. Using deep pyrosequencing, we studied cloacal microbiome (CM) composition in free living barn swallows (Hirundo rustica), a long-distance migratory passerine bird. Barn swallow CM was dominated by bacteria of the Actinobacteria, Proteobacteria and Firmicutes phyla. Bacteroidetes, which represent an important proportion of the digestive tract microbiome in many vertebrate species, was relatively rare in barn swallow CM (< 5%). CM composition did not differ between males and females. Our data support a correlation between CM in breeding pair individuals, supporting the hypothesis that cloacal contact during within-pair copulation may promote transfer of bacterial assemblages. The importance of this factor on CM composition was of relatively low effect size, however, possibly due to the species high level of sexual promiscuity