Despite their potential ecological and evolutionary importance, factors shaping the composition of bacterial communities in wild vertebrate populations remain poorly understood. The goal of this study was to examine the relative contributions of environmental factors and genetic factors (e.g. species and common origin) to the variation of cloacal bacterial assemblages in wild bird nestlings. We conducted a partial cross-fostering experiment with two passerine species, the great tit Parus major and the blue tit P. caeruleus, sharing similar habitats and breeding biology. Nestlings of the two species were exchanged four days after hatching and cloacal bacteria were sampled nine days later. The structure of cloacal bacterial communities was determined by Ribosomal Intergenic Spacer Analysis. Our results showed that each nestling displayed a unique bacterial community. Furthermore, nestlings raised in the same nest shared significantly similar bacterial communities. The similarity of bacterial community was higher among heterospecific siblings raised within the same nest than between biological siblings raised in separate nests. Effects of common origin between species could not be detected and, if present, were dominated by nest-based short-term environmental effects. Our results show that growth conditions within nests and individually based endogenous factors have significant effects on cloacal bacteria assemblages and could affect post-fledging condition.