Allergic rhinitis and asthma are major public health concerns with growing evidence of associations with upper airway dysbiosis. This study used 16S rRNA sequencing to characterize the oral bacteriome of 344 individuals with allergic rhinitis (AR), allergic rhinitis with asthma (ARAS), asthma (AS), and healthy controls (CT). Four abundant phyla and ten dominant genera differed significantly between disease groups and controls. Bacteriome composition showed distinct differences in microbial structure (beta-diversity) between each disease group and controls. Network analysis revealed that AR and ARAS bacteriomes had more complex webs of microbial interactions than healthy controls, with alterations in bacterial connectivity potentially related to chronic respiratory disease.