Anemia following allogeneic hematopoietic stem cell transplantation (HCT) can be immune- or non-immune mediated. Auto- or alloimmunity due to blood groups incompatibility remain an important cause if post-HCT immune-mediated anemia. ABO incompatibility is commonly encountered in HCT and may lead to serious clinical complications including acute hemolysis, pure red cell aplasia, and passenger lymphocyte syndrome. It remains controversial whether ABO incompatibility may affect HCT outcomes, such as relapse, non-relapse mortality, graft-versus-host disease and survival. Non-ABO incompatibility is less frequently encounterd but can have similar complications to ABO incompatibility, causing adverse clinical outcomes. It is crucial to identify the driving etiology of post-HCT anemia in order to prevent and treat this condition. This requires a comprehensive understanding of the mechanism of anemia in blood group incompatible HCT, and the temporal association between HCT and anemia. In this review, we summarized the literature on post-HCT immune-mediated anemia with a focus on ABO and non-ABO blood group incompatibility, described the underlying mechanism of anemia, and outlined preventive and treatment approaches.