In this study, we used RNA-Seq for comparative transcriptome profile analysis of the heterogeneity in IgM+ cell subsets from PBL of Nile tilapia, including IgM-, IgMlo and IgMhi lymphocytes. The information of transcriptome sequences and differentially-expressed genes related to innate immunity may contribute to further understanding of B cell activity and the characterization of different B cell subsets in teleost fish.