Monitoring engraftment of donor cells after allogeneic transplantation is the key of assessing successful establishment of animal transplantation model. The purpose of this study was to establish a method for analysis of chimerism in rhesus transplantation model. Y-specific sequence in rhesus was amplified by the polymerase chain reaction (PCR), method for analysis of chimerism in rhesus after sex-mismatched transplantation was established; the feasibility and sensitivity of the approach were tested by using serial DNA mixtures of sex-mismatched individuals; the accuracy of results was confirmed by chromosome karyotype analysis simultaneously; Chimerisms of one rhesus received allogeneic stem cell transplantation and the other received mesenchymal stem cells (MSC) transfusion were detected by this method. The results showed that a 176 bp long sequence of PCR product was gained in male rhesus, while no product was gained in female rhesus. The sensitivity of this method was up to 0.05% (male/female DNA ratio). Male donor chimerism were found on day 7 and 14 after allogeneic stem cell transplantation by Y-specific sequence and chromosome karyotype analysis. Otherwise, male donor chimerism was found in peripheral blood at 1 hour and in bone marrow on day 30 after MSC transfusion by this method, but no male donor chimerism was found after MSC transfusion using chromosome karyotype analysis. In conclusion, this rapid, sensitive approach can used to assess chimerism in experiments of rhesus alloorgan transplantation and cell transfusion.