A neurotoxin, homoanatoxin-a, was identified from a toxic strain of the cyanobacterium Raphidiopsis mediterranea Skuja (strain LBRI 48) isolated from Lake Biwa, Japan, as the major toxin component (0.57% of dry cell-weight). This cyanobacterium produced anatoxin-a and a new homoanatoxin-a derivative as minor components (0.04 and 0.06%, respectively). The structure of a new compound was assigned based on the spectral data as 4-hydroxyhomoanatoxin-a, which was not toxic to mice up to 2.0 mg/kg by intraperitoneal injection. The isolation of minor components was accomplished by improved extraction and separation procedures: (1) extraction with methanol-water (4:1) from dried cells, (2) adsorption of aqueous residue on ODS column (or cartridge) after evaporation of methanol, (3) cleaning up of the column by successive elution with water and 50% methanol/water, (4) elution of a toxic fraction by 20% methanol/water containing 0.1% TFA and (5) HPLC (ODS) purification with methanol/water containing 0.05% TFA. The procedures were effective in removing impurities and concentrating alkaloidal neurotoxins. It should be noted that this is the first report demonstrating the simultaneous production of anatoxin-a and homoanatoxin-a by the same strain of cyanobacterium.