Follicular (FO) B cells and marginal zone (MZ) B cells belong to the mature B cell population in spleen of mice. To identify new surface markers of these mature B cell subsets, we compared gene expression profiles of FO and MZ B cells by DNA microarray using FACS-sorted mouse FO and MZ B cells. From 14,000 mouse genes, 27 membrane proteins were expressed mainly in MZ B cells while another 22 membrane proteins expressed largely in FO B cells. Using FACS analysis, we identified that CD36, CD68, and CD49e were expressed on MZ B cells but not on FO B cells. In addition, using semi-quantitative PCR, we found that the mRNA of CD131 were much more abundant in MZ B cells. These results revealed new phenotypic properties of MZ and FO B cells, and would facilitate further studies in the differentiation and functions of these mature B cells.