Cyanobacterial blooms that generate microcystins (MCs) are being increasingly recognized as a potent health hazard in aquatic ecosystems. However, immunomodulation induced by cyanotoxins has not been well documented. This paper reports the in vivo data on the immune disorder caused by crude microcystin (MC) extract of cyanobacteria blooms collected from Taihu Lake, China, with respect to cytokine mRNA levels. Using reverse-transcriptional polymerase chain reaction (RT-PCR), the expression of multiple cytokines, including proinflammatory (IL-1beta, TNF-alpha, and IL-6) and Th1/Th2-related cytokines (IL-2, IL-4 and IL-10), was evaluated following the cyanobacteria blooms extract containing MCs (CBE) exposure at four doses of 23, 38, 77, 115 mg lyophilized algae cells/kg body weight. The results showed that the mRNA levels of TNF-alpha, IL-1beta, IL-2 and IL-4 decreased significantly following injection of all doses as compared to the control (LPS or ConA only), while the IL-6 level was unaffected. Contrast to this decrease, the level of IL-10 mRNA was, however, transiently up regulated following injection of the lowest dose of CBE. The distinct patterns of expression of these cytokines suggested a modulation of cytokine network, the essential component of the host immune system. We further developed a mathematical model to simulate the interaction of T helper cell subsets and related cytokines, which proved to be a good approach to study the kinetics of the interaction of cells and cytokines in microcystin immunosuppression.