Two major classes of B lymphocytes have been described to date in rainbow trout: IgM + and IgT + cells. IgM + cells are mainly localized in the spleen, peripheral blood and kidney but are also found in other tissues. However, differences among IgM + cell populations attending to its location are poorly defined in fish. Thus, the aim of this work was to characterize the expression of different immune molecules such as chemokine receptors, Toll-like receptors (TLRs) and transcription factors on sorted IgM + lymphocytes from different rainbow trout tissues. IgM + populations from blood, spleen, kidney, gills, intestine and liver were isolated by cell sorting and the constitutive levels of transcription of these genes evaluated by real-time PCR. To further characterize B cells, we identified an MS4A sequence. In humans, the MS4A family includes several genes with immune functions, such as the B cell marker CD20 or FcRβ. Subsequently, we have also evaluated the mRNA levels of this MS4A gene in the different IgM + populations. The relevant differences in transcriptional patterns observed for each of these IgM + populations analyzed, point to the presence of functionally different tissue-specific B cell populations in rainbow trout. The data shown provides a pattern of genes transcribed in IgM + B cells not previously revealed in teleost fish. Furthermore, the constitutive expression of all the TLR genes analyzed in IgM + cells suggests an important role for these cells in innate immunity.