This study was aimed to compare the immunoregulatory effects of mesenchymal stem cells derived from human umbilical cord amnion (AMSC) and adult bone marrow (BMMSC) in vitro, so as to provide the experimental basis for allogeneic hematopoietic stem cell transplantation in clinic. The AMSC were isolated from human umbilical cord amnion by using digestion with collagenase. They were identified by morphology, growth characteristics, immunophenotyping and differentiation ability. Furthermore, the immunoregulatory effects of AMSC and BMMSC were tested by lymphocyte transformation and mixed lymphocyte reaction. The results showed that AMSC and BMMSC possessed similar biological characteristics such as exhibition of fibroblastic morphology and strong proliferation ability in vitro. Flow cytometric analysis revealed that the AMSC highly expressed CD73, CD90, CD105, but negative for CD34, CD45, HLA-DR, and CD86 of BMMSC. Functionally, they all could differentiate into adipocyte, osteocytes and chondrocytes. Moreover, AMSC could inhibit cellular or nonspecific mitogenic stimuli-induced T cell proliferation with a dose-dependent manner. Reverse transcriptional-polymerase chain reaction also demonstrated expression of the similar immune cytokines in AMSC and BMNSC. It is concluded that the MSC derived from human umbilical cord amnion may be an excellent alternative source for experimental and clinical application.