Allogeneic hematopoietic bone marrow transplantation (BMT) is an established and curative treatment for many aggressive hematological malignancies. However, the success of allogeneic BMT is limited by graft versus host disease (GVHD) due to the attack of recipient organs. There is growing evidence that the commensal microbiota is dysregulated following allogeneic BMT. Recent studies have made significant strides in examining the role of the host and donor microbiome on GVHD severity and pathogenesis. In this review, we summarize the current knowledge of the complex roles of the microbiome on GVHD, as well as the role of the metabolome through which it confers its effects.