The pathogenesis of the inflammatory bowel disease (IBD) is linked to an activation of the gastro-intestinal immune system toward the gut microbiota in genetically susceptible hosts and under the influence of the environment. The microbial community in the human gastrointestinal tract is fundamental to the health. Loss of the fragile equilibrium within this complex ecosystem, termed dysbiosis, is involved in numerous pathologies, including IBD. Patients with IBD exhibit an altered gut microbiota composition with notably a decreased abundance of anti-inflammatory bacteria such as Faecalibacterium prausnitzii. We also observed alteration in the fungal microbiota composition in these patients. The association of several polymorphisms of innate immunity genes involved in microbial sensing with IBD is another argument for the involvement of the gut microbiota in the IBD pathogenesis. Some genetic factors involved in IBD might indeed act through a microbiota effect. We notably demonstrated that this is the case for the IBD susceptibility gene CARD9. Based on its demonstrated role in IBD pathogenesis, the gut microbiota is now considered as a potential therapeutic target and next generation probiotics as well as fecal microbiota transplantation are actively investigated.