Marginal zone (MZ) B cells differ from follicular (FO) B cells in their functional, phenotypic and localization properties. It is still unclear whether B cells from the MZ compartment also have distinct or biased BCR specificities, recognizing only a limited number of conserved antigenic structures. To address the complexity of the immune response mounted by marginal zone B cells, we compared the antibody repertoire of murine MZ and FO B cells induced by immunization with two different virus-like particles (VLPs). Antibody sequences isolated from sorted VLP-specific MZ and FO B cells were similar in heavy chain V, D and J gene segment usage. Sequence analysis of CDR3 regions of antibodies from MZ and FO B cells also revealed no consistent difference in N nucleotide additions or CDR3 length. In contrast, somatic hypermutations were reduced in CDR regions of antibodies from MZ B cells compared to those from FO B cells. These results indicate that the response of MZ B cells to VLPs is clonotypically heterogeneous and suggest that the MZ B cell compartment is capable of generating variable and diverse antibody responses.