Microcystis aeruginosa is a common cyanobacterium in water blooms that appear world widely in eutrophic freshwaters, and its toxic blooms have caused many death and illness cases. This paper presents the first data on the immunotoxicity of a microcystin (MC) extract of cyanobacteria bloom collected from Taihu Lake, China to BALB/c mice. The cyanobacteria bloom extract (CBE) containing MCs was administered by i.p. injection for 14 days at three sublethal doses of 16, 32, 64 mg lyophilized algae cells/kg body weight. Exposure to CBE decreased body weights dose-dependently. Meanwhile, liver body weight ratios were markedly increased. The significant differences were also observed in spleen and thymus body ratios upon the elevation of treatment dose comparing to control. CBE was also found to reduce the phagocytosis evaluated using phagocytic index of peritoneal phagocyte; this suppression was not evident in percentage phagocytosis. Treatment of CBE produced the inhibition of lipopolysaccharide-induced lymphoproliferation and the dose-dependent decrease of the numbers of antibody-forming cells in mice that were immunized by using T-dependent antigen sheep red blood cells. However, CBE did not affect concanavalin A-induced T cell proliferation. Our results demonstrate that exposure to CBE resulted in immunosuppression in mice.