Diversity of the gut bacterial community is of prime importance for optimal food digestion and, therefore, for nutritional condition of avian nestlings. Consequently, bacterial community should be considered as a predictor of the future survival and recruitment of young birds. To explore this hypothesis, we studied the cloacal microbiota, by using RISA procedure, in two avian species sharing environmental conditions during growth, the avian brood parasitic great spotted cuckoo Clamator glandarius, and their main host in Europe, the magpie Pica pica. As estimates of phenotypic condition of nestlings we studied two nutrition-dependent traits, the immune response to an innocuous antigen (phytohemagglutinin), and the residuals of body mass on tarsus and wing length of nestlings. According to the hypothesis, we found significant relationships between microbial diversity and nestling phenotypic traits related to probability of recruitment. Briefly, both magpie and cuckoo nestlings having more similar microbial diversity were also those with similar immune response and body condition index respectively. Our results show a possible association between bacterial communities and variables related to the probability of post-fledging survival and recruitment of birds, as well as possible reasons explaining magpie-cuckoo differences in the nutritionally conditioned variables better associated with their bacterial diversity.