The host gut microbiome functions in digestion and immune defense, but additionally influences cognitive behavior. Habitat and diet are strong influencers in shaping the gut microbiome. However, among closely related species, phylogenetic relatedness is a strong predictor of gut microbiome community composition. Although phylogeny is a strong predictor, the impact hybridization has on the gut microbiome is poorly known. To explore this, we sampled feces from nestlings across a hybrid zone transect for black-capped (Poecile atricapillus) and Carolina chickadees (Poecile carolinensis) during the 2021 and 2022 breeding seasons. These nestlings were brought back to the Lehigh University Animal Facility and raised to adulthood under common conditions for cognitive testing. Fecal samples were taken at multiple time points and used to characterize the gut microbiome community composition. To do this, we extracted microbial DNA and sequenced the V3-V4 region of the 16S rRNA gene. Using amplicon sequence variants (ASVs), we compared the abundance and diversity of bacterial taxa across ancestry groups and at different time points after experiencing common conditions. Being raised under common conditions led to a decreased alpha diversity for parental species, but not for hybrids. After standardizing environmental conditions, differences between ancestry groups in abundance of specific gut phyla and specific ASVs suggests that genetic variation also plays a significant role in gut microbial composition. Alpha diversity and abundance of individual ASVs seemed to correlate with cognitive performance as well. Assessing the factors that influence gut microbiome diversity in two closely related sister species and their hybrids helps us to better understand the various factors that shape host-microbiome communities.