Inflammatory bowel disease (IBD) is a complex multi-factorial chronic relapsing disease of the digestive tract where dysbiosis of autochthonous intestinal microbiota, environmental factors and host genetics are implicated in the disease development, severity, course and treatment outcomes. The two clinically well-defined forms of IBD are Crohn's disease (CD) and ulcerative colitis (UC). The CD affects the local immune response of the entire gastrointestinal tract whereas the inflammation in UC is mainly restricted to the colonic mucosa. Prolong progressive inflammation due to CD and UC often lead to colonic cancer. In healthy individuals, the enormous taxonomic diversity and functional potency of gut microbiota including members from the bacterial and fungal microbiota tune the host immunity and keep the gastric environment beneficial and protective. However, expansion of pathobionts, autochthonous microbes with the potency of pathogenicity in dysbiotic condition, in the gastrointestinal tract and subsequently enriched inflammatory microbial products in the gastrointestinal milieu attract different immune cells and activate aberrant host immune response which leads to excessive production and secretion of different cytokines that damage the colonic epithelial cells and manifest chronic inflammatory digestive disease. In the current chapter, we provided our updated understanding about the different bacterial and fungal pathobionts, their genomic and metabolic signatures, and geo-specific diversity of gut microbes linked with IBD across the globe at the molecular resolution. An improved understanding of IBD and the factors associated with the disease will be a boost for therapeutic development and disease management.