Objective To discriminate whether chemical compounds are micronuclei-inducing by counting the ratio of bone marrow micronucleus polychromatic erythrocytes (MNPCE) dyed with a single fluorescence reagent (acriding organe, AO) by single-laser flow cytometry. Methods Treating male KM mice and SD rat with cyclophosphamide (CP) respectively, and counting their frequencies of micronucleated polychromatic erythrocytes (MNPCE) as well as frequencies of micronucleated normochromatic erythrocytes (MNNCE) in bone marrow by AO and a single_laser flow cytometer (FCM), comparing and analyzing the results from different methods. Results The results showed that, along with increasing dose of CP, the ratio of MNPCE also corresponding increase, suggesting significant quantative-efficiency correlation. MNPCE were also counted manually by fluorescence microscopy, and the results showed no significant difference with that by flow cytometry. Conclusions AO_FCM fully automated detection method for the detection of MNPCE and MNNCE in mice and rat bone marrow micronucleus rate is reliable.