Gut microbiota inhabit the host gastrointestinal (GI) tract and play roles in many aspects of metabolic and immunologic homeostasis. Understanding about gut microbiota composition in health and disease is accumulating with the advances in gene sequencing technology. Graft-versus-host disease (GVHD) is a major complication after allogenic bone marrow transplantation (allo-BMT), a gold standard clinical procedure to treat hematologic disorders such as leukemia and lymphomas. Recent studies have shown that a disturbance in the gut microbiota affects GVHD prognosis. Decrease in a compositional diversity is suggested as an independent predictor of GVHD and colonization of noncommensal Enterococcus is shown to be involved in unpleasant treatment outcomes. This article describes current understanding about allo-BMT-induced gut microbiota changes and its involvement in the incidence of GVHD. In addition, several putative therapeutic strategies to decrease GVHD-related mortality after allo-BMT are discussed.