Mature B cells in the spleen of mouse and human comprise of two main subsets, the follicular (Fo) B cells and the marginal zone (MZ) B cells. In this study, we report that Fo and MZ B cells express different levels of DNA methyltransferase Dnmt3a. By using RT-PCR and immunohistochemistry, we found that Fo B cells expressed high level of Dnmt3a while MZ B cells expressed little. Treatment of mice by in vivo administration of 5'-azacytidine, an inhibitor of DNA methyltransferases, induced B cell loss in both the bone marrow and the spleen. We noticed that this treatment resulted in a much faster and more severe disappearance of Fo B cells than MZ B cells in the spleen. Further analysis showed that MZ progenitors increased significantly in mice treated with 5'-azacytidine. These results suggest that epigenetic mechanisms involving Dnmt3a might participate in the development of B cells including the differentiation of Fo B cells and MZ B cells in the periphery.