There is an increasing amount of knowledge on the cytotoxic properties of cyanotoxins, but relatively little is known regarding their fine specificity and mechanisms of action. In this study, we investigated the influence of microcystin-LR and AnTx-a on mouse B- and T-lymphocyte subpopulations in vitro. Cyanotoxins significantly decreased the cell viability after 4 and 24 h, compared to the untreated control. After 24 h exposure to microcystin-LR and anatoxin-a, the viability of splenocytes dropped to 23% and 57%, respectively. Our data demonstrate that microcystin-LR induced apoptosis specifically in mouse B cells, probably via the B-cell antigen receptor and mitochondrial pathway, while the T cells were not affected. AnTx-a showed cytotoxic effects on both lymphocyte subpopulations, but the effects were driven by mechanisms different from apoptosis. These findings demonstrate that the cyanotoxins could cause cytotoxic alterations in a variety of cell types different from the major targets, operating via distinct mechanisms.