Inflammatory bowel diseases [IBD], ulcerative colitis [UC] and Crohn's disease [CD], are chronic intestinal disorders of unknown etiology. UC and CD are heterogeneous diseases characterized by various genetic abnormalities that lead to overly aggressive T-cell responses to a subset of commensal enteric bacteria in genetically susceptible individuals. As one of critical factors involved in pathogenesis of IBD, relative imbalance of aggressive and protective bacterial species, termed dysbiosis, has been reported by various literatures. Since early days of microbiology, representatives of microbial species [over 400 species] have been isolated from human gastrointestinal tract, and analyses of dysbiosis in IBD were mainly dependent on culture techniques. However, recent molecular ecological studies based on ribosomal RNA [rRNA] sequences have revealed that cultivation has been able only to access a small fraction of the microbial diversity within the gastrointestinal tract. These techniques enable characterization and quantification of the microbiota. Clone libraries enable identification of the composition of the microbiota. Microbial community structure can be analyzed via fingerprinting techniques, and dot blot hybridization or fluorescent in situ hybridization can analyze abundance of particular taxa. Recent report shows a systematic framework of the microbial diversity in the human gut of more than 1000 different species-level phylogenetic types [phylotypes]. This review focuses on recent advances in the molecular ecological approaches for studying the gut microbiota in IBD.