<jats:title>Abstract</jats:title><jats:p>Crohn’s disease causes chronic inflammation in the gastrointestinal tract and its pathogenesis remains unclear. In the intestine of Crohn’s disease patients, CD14<jats:sup>+</jats:sup>CD11<jats:sup>+</jats:sup>CD163<jats:sup>low</jats:sup> macrophages contribute to inflammation through the induction of Th17 cells and production of inflammatory cytokines; the CD14<jats:sup>+</jats:sup>CD11c<jats:sup>+</jats:sup>163<jats:sup>high</jats:sup> fraction is anti-inflammatory through the production of IL-10 in normal cases. In this report, the 16S rRNA gene amplicon sequencing method was used to identify bacteria that are specifically present in intestinal CD14<jats:sup>+</jats:sup>CD11c<jats:sup>+</jats:sup> macrophages of Crohn’s disease patients. Bacteria present in intestinal CD14<jats:sup>+</jats:sup>CD11c<jats:sup>+</jats:sup> macrophages and mucus of Crohn’s disease patients were separated into different clusters in principal coordinates analysis. There was a statistically significant increase in the relative composition of CD14<jats:sup>+</jats:sup>CD11c<jats:sup>+</jats:sup> macrophages from mucus in two phyla (<jats:italic>Proteobacteria</jats:italic> [p = 0.01] and <jats:italic>Actinobacteria</jats:italic> [p = 0.02]) and two families (<jats:italic>Moraxellaceae</jats:italic> [p < 0.001] and <jats:italic>Pseudomonadaceae</jats:italic> [p = 0.01]). In addition, OTU-1: <jats:italic>Acinetobacter</jats:italic> and OTU-8: <jats:italic>Pseudomonadaceae</jats:italic> tended to concentrate in the CD14<jats:sup>+</jats:sup>CD11c<jats:sup>+</jats:sup>CD163<jats:sup>low</jats:sup> subset, whereas OTU-10: <jats:italic>Proteus</jats:italic>, OTU-15: <jats:italic>Collinsella</jats:italic> tended to concentrate more in the CD14<jats:sup>+</jats:sup>CD11c<jats:sup>+</jats:sup>CD163<jats:sup>high</jats:sup> subset than the other subset and mucus.</jats:p>