The intestinal microbiota is a key antigenic driver in Crohn's disease CD. We aimed to identify changes in the gut microbiome associated with, and predictive of, disease recurrence and remission. A total of 141 mucosal biopsy samples from 34 CD patients were obtained at surgical resection and at colonoscopy 6 and/or 18 months postoperatively; 28 control samples were obtained: 12 from healthy patients healthy controls and 16 from hemicolectomy patients surgical controls. Bacterial 16S ribosomal profiling was performed using the Illumina MiSeq platform. CD was associated with reduced alpha diversity when compared with healthy controls but not surgical controls p < 0.001 and p = 0.666, respectively. Beta diversity composition differed significantly between CD and both healthy p < 0.001 and surgical p = 0.022 controls, but did not differ significantly between those with and without endoscopic recurrence. There were significant taxonomic differences between recurrence and remission. Patients experiencing recurrence demonstrated elevated Proteus genera p = 0.008 and reduced Faecalibacterium p< 0.001. Active smoking was associated with elevated levels of Proteus p = 0.013 postoperatively. Low abundance of Faecalibacterium < 0.1% and detectable Proteus in the postoperative ileal mucosa was associated with a higher risk of recurrence (odds ratio OR 14 1.7-110, p = 0.013 and 13 1.1-150, p = 0.039, respectively) when corrected for smoking. A model of recurrence comprising the presence of Proteus, abundance of Faecalibacterium, and smoking status showed moderate accuracy (area under the curve AUC 0.740, 95% confidence interval CI 0.69-0.79). CD is associated with a microbial signature distinct from health. Microbial factors and smoking independently influence postoperative CD recurrence. The genus Proteus may play a role in the development of CD.