Neurotoxins β-N-methylamino-L-alanine (BMAA) and its isomer 2,4-diaminobutyric acid (DAB) have been reported previously in diverse strains of cyanobacteria. In this study, BMAA and DAB were analyzed for two strains of Microcystis aeruginosa incubated with four different levels of phosphate, nitrate, illumination, and temperature, respectively, in order to explore the effects of growth factors on toxin-producing ability of cyanobacteria. Both toxins were also screened in 17 cyanobacterial strains cultured with BG-11 medium and conventional illumination and temperature conditions, and in three field phytoplankton samples collected from different lakes in China. All samples were analyzed using a liquid chromatography-tandem quadrupole mass spectrometry (LC-MS/MS) system coupled with a hydrophilic interaction liquid chromatography (HILIC) column. Results showed that no BMAA was detected in any of the cyanobacterial strains grown under our laboratory culture conditions, or in any of the field samples. Production of DAB in M. aeruginosa was significantly enhanced by extreme concentrations of nutrient and physical factors. Various concentrations of DAB were also present in most cultured samples (13 of 17) of cyanobacteria and were not species specific. This is the first time to report the production of DAB in M. aeruginosa cultured under alterative conditions in laboratory. Occurrence of DAB in most of the strains examined here means that consideration should be given to the presence of this compound in freshwater environment in China.