Objectives/HypothesisThe adenoid pad has been considered a reservoir for bacteria in the pathogenesis of otitis media with effusion. This study aimed to characterize the middle ear microbiota in children with otitis media with effusion and establish whether a correlation exists between the middle ear and adenoid microbiota.Study DesignProspective, controlled study.MethodsMiddle ear aspirates adenoid pad swabs were collected from 23 children undergoing ventilation tube insertion. Adenoid swabs from patients without ear disease were controls. Samples were analyzed using 16S rRNA sequencing on the Illumina MiSeq platform.ResultsThirty‐five middle ear samples were collected. The middle ear effusion microbiota was dominated by Alloiococcus otitidis (23% mean relative abundance), Haemophilus (22%), Moraxella (5%), and Streptococcus (5%). Alloiococcus shared an inverse correlation with Haemophilus (P = .049) and was found in greater relative abundance in unilateral effusion (P = .004). The microbiota of bilateral effusions from the same patient were similar (P < .001). However, the otitis media with effusion microbiota were found to be dissimilar to that of the adenoid (P = .01), whereas the adenoid microbiota of otitis media with effusion and control patients were similar (P > .05) (permutational multivariate analysis of the variance).ConclusionsDissimilarities between the local microbiota of the adenoid and the middle ear question the theory that the adenoid pad is a significant reservoir to the middle ear in children with otitis media with effusion. A otitidis had the greatest cumulative relative abundance, particularly in unilateral effusions, and shares an inverse correlation with the relative abundance of Haemophilus.Level of EvidenceNA Laryngoscope, 126:2844–2851, 2016