Plumage bacteria might influence the trade-off between parental and self-preening efforts in birds, therefore affecting breeding success. However, too little is known about natural variation patterns in plumage bacterial communities for these hypotheses to be thoroughly assessed. We studied the density and phylotypic richness of plumage bacterial assemblages in wild breeding populations of Pied Flycatchers Ficedula hypoleuca and Great Tits Parus major in the same area and breeding season, using flow cytometry and ribosomal intergenic spacer analysis (RISA). The density of plumage bacteria was higher in Tits than in Flycatchers, providing evidence that bacterial microflora differs even between co-occurring hosts that share habitat, nest site and foraging preferences. It is concurrent with the finding that migratory birds might have lower bacterial loads than sedentary birds. In both species bacterial loads were higher in females than in males, which along with two earlier studies, indicates the generality of this sex pattern. A negative correlation between parental body mass and the richness of feather-degrading bacterial phylotypes was found in Pied Flycatchers. In Great Tits, higher bacterial densities in the plumage of parent birds were associated with the production of fewer fledglings. However, the causality of these associations remains to be tested experimentally.