Anatoxin-a (1) is the first neurotoxin obtained from a freshwater cyanobacterium, Anabaena flos-aquae and has a high toxicity (LD50, i.p., mouse: 200 µg/kg). 1 has occurred limitedly in North America and northern Europe and no occurrence has been reported in Japan so far. Thermospray-liquid chromatography/mass spectrometry (TSP-LC/MS) was applied to the analysis of trace amount of 1 together with its degradation product (2) after the following optimizations: HPLC conditions, TSP operating conditions, slight modification of the reported clean-up method using a tandem cartridge system and introduction of acetyltropin as an internal standard. The established TSP-LC/MS is of great advantage to the conventional HPLC-UV and the detection limit was 500 pg. The method was used for trace analysis of 1 and 2 in laboratory strains and bloom samples and made possible the first detection of them in Japanese samples.