Nitrogen causes the frequent occurrence of harmful algal blooms and possible microcystin production. The effects of ammonia and alanine (Ala) on the growth and microcystin production of Microcystis aeruginosa were investigated using an isotope tracer ((15)N). The results indicated that Ala was directly used by M. aeruginosa and contributed to biomass formation amounting to 2.1 × 10(7) cells mL(-1) on day 48, compared with only 6.2 × 10(6) cells mL(-1) from ammonia alone. Microcystin-LR production with Ala was less than that of ammonia, which peaked at 50.2 fg cell(-1) on day 6. Liquid chromatographic analysis with tandem mass spectrometry of (15)N-microcystin-LR suggested that (15)N from ammonia was probably synthesized into the arginine residue. By contrast, (15)N from Ala was assimilated into the Ala, leucine, the iso-linked (2R,3S)-3-methylaspartic acid, arginine, and certain unusual C20 amino acid residues. The results represent the forward steps in the determination of the nitrogen forms that fuel toxin production and blooms.