Marginal zone and B1 B-cells have the capacity to respond to foreign antigens more rapidly than conventional B-cells, providing early immune responses to blood-borne pathogens. Ly9 (CD229, SLAMF3), a member of the SLAM family receptors, has been implicated in the development and function of innate T lymphocytes. Here, we provide evidence that in Ly9-deficient mice splenic transitional T1, marginal zone and B1a B cells are markedly expanded, whilst development of B lymphocytes in bone marrow is unaltered. Consistent with an increased number of these B cell subsets, we detect elevated levels of IgG3 natural antibodies, and a striking increase of T-independent type II antibodies following immunization with TNP-Ficoll in the serum of Ly9-deficient mice. The notion that Ly9 could be a negative regulator of innate-like B cell responses was supported by the observation that administering a mAb directed against Ly9 to WT mice selectively eliminated splenic marginal zone B cells and significantly reduced the numbers of B1 and transitional T1 B cells. Additionally, Ly9 mAb dramatically diminished in vivo humoral responses and caused a selective down-regulation of the CD19/CD21/CD81 complex on B cells and concomitantly an impaired B cell survival and activation in a Fc-independent manner. We conclude that altered signaling due to the absence of Ly9 or induced by anti-Ly9 may negatively regulate development and function of innate-like B cells by modulating B cell activation thresholds. The results suggest that Ly9 could serve as a novel target for the treatment of B cell related diseases.