In general, animal species harbor distinct microbiomes and the similarities of these communities mirror host phylogeny: an eco-evolutionary pattern known as phylosymbiosis. However, the ubiquity and strength of phylosymbiosis in avian microbiomes are weak and remain poorly understood. Avian brood parasites provide unique opportunities to investigate the roles of genetics vs. environment as both species’ nestlings are raised in the same nest, on the same diet, and by the same parents. We utilized a model of two passerines (from order Passeriformes), the obligately interspecific brood parasite Brown-headed Cowbird Molothrus ater (BHCO) and one of its hosts, the Prothonotary Warbler Protonotaria citrea (PROW), to investigate how species identity and parasitism affects the gut host-associated bacterial microbiome (HAMB) of the developing nestlings. We sampled the fecal microbiome of wild BHCO nestlings and PROW nestlings from both parasitized and unparasitized nests. While we were able to detect significant influences of sampling locality, we found that the presence or absence of a brood parasite nestling did not significantly alter the developing HABM of the PROW nestlings. Further, the fecal HAMB of BHCO and PROW were indistinguishable from one another. Our findings run contrary to those found in other brood parasite systems where hosts and parasites represented different taxonomic orders. Thus, rearing environment may be especially important in determining the microbiome of brood parasite nestlings, and genetics are not strongly influencing the parasite HAMB at this early stage in life.