Objective This study compares the population and repair ability of bone marrow hematopoietic stem cells (HSCs) and mesenchymal stem cells (MSCs) in experimental colitis (EC) rat model after allogeneic stem-cell transplantation (SCT). Methods EC was induced by 2, 4, 6-trinitrobenzenesulfonic acid (TNBS). The HSCs, MSCs, HSCs+MSCs, derived from male Sprague-Dawley rats, were cultured and labeled with bromodeoxyuridine and then transplanted into the EC rat. The colon samples were collected for histologic evaluation at days 7, 14, and 21 posttransplantation. Immunohistochemical staining, polymerase chain reaction, and fluorescence in situ hybridization were used to detect donor stem cells population. Results EC induced by TNBS had characteristics similar to those of Crohn's disease. A large number of bromodeoxyuridine-labeled HSCs or MSCs were detected on days 7, 14, and 21 posttransplantation. Sex-determining region of Y chromosomes (sry) was found in all EC regions, but not in control and normal tissues. A clear localization of Y chromosomes in the colons of EC rat was detected by fluorescence in situ hybridization. Immunohistochemical staining revealed that HSCs or MSCs had similar population ability. When HSCs and MSCs were combined, gross morphologic scores significantly improved 21 days post-SCT compared with the control without SCT, but only slightly better than that of HSCs or MSCs alone. Conclusions Allogeneic transplantation of HSCs or MSCs alone could populate in the injured regions of the colons, both showed similar population ability in the colons of the TNBS-induced EC model rats. Combination transplantation of HSCs with MSCs could improve the gross morphologic scores of EC.