Background Microbes and allergens can stimulate the nasal mucosa, potentially leading to the development of acute bacterial rhinosinusitis (ABRS). This study was designed to determine if allergen exposure alters the sinonasal microbiome. Methods We performed a parallel observational study of healthy adults with seasonal allergic rhinitis (SAR; grass or tree, n = 20) or nonallergic subjects (n = 19). Microbiota specimens were obtained by endoscopy from the middle meatus and vestibule before and during the relevant season and were analyzed by terminal restriction fragment length polymorphism analysis. Differences in bacterial microbiota were assessed by standard ecological measures of bacterial diversity. Quality of life and symptom scores were recorded, and nasal lavages for eosinophils were performed. Results SAR subjects had increased nasal symptoms in season, impaired disease-specific quality of life, and increased nasal eosinophils, compared with no changes in nonallergic subjects. During the season, SAR subjects had a significantly greater variety of organisms in the middle meatus compared with nonallergic subjects (p < 0.036) and increased bacterial diversity (Shannon index, p < 0.013). We found a significant positive correlation between bacterial diversity in the middle meatus during the season and the nasal lavage eosinophil count of SAR subjects. There were no significant changes in the nasal vestibule (p > 0.05, all comparisons). Conclusion The interaction of allergy and microbiota may affect the sinonasal physiology, with broad implications for several airway diseases. Characterization of the specific organisms involved using next-generation sequencing may clarify the relationship between allergic inflammation and ABRS. This finding may help explain why allergic inflammation predisposes to ABRS.