Inflammatory bowel disease (IBD) is a chronic immune‐mediated intestinal disease consisting of ulcerative colitis and Crohn's disease. Inflammatory bowel disease is believed to be developed as a result of interactions between environmental, immune‐mediated and microbial factors in a genetically susceptible host. Recent advances in high‐throughput sequencing technologies have aided the identification of consistent alterations of the gut microbiome in patients with IBD. Preclinical and murine models have also shed light on the role of beneficial and pathogenic bacteria in IBD. These findings have stimulated interest in development of non‐invasive microbial and metabolite biomarkers for predicting disease risk, disease progression, recurrence after surgery and responses to therapeutics. This review briefly summarizes the current evidence on the role of gut microbiome in IBD pathogenesis and mainly discusses the latest literature on the utilization of potential microbial biomarkers in disease diagnosis and prognosis.