Tetrodotoxin (TTX), a powerful sodium channel blocker, usually exists as a mixture of its analogs (TTXs) in natural sources. Due to the structural variation, some analogs are difficult to detect using the postcolumn liquid chromatography-fluorescent detection (LC-FLD) system. Liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS) analysis of TTXs can be achieved by a combination of chromatography on a reversed-phase column with long carbon chains (C30) and the mobile phase containing an ion pair reagent (ammonium heptafluorobutyrate). The relationship between the amount of applied standard TTX and its peak area on the mass chromatogram (m/z 320) showed good linearity over a range of 50-1000 pmol. The detection limit for TTX in the selected ion monitoring (SIM) mode was estimated to be 0.7 pmol (signal to noise ratio: 2). The tandem mass spectrometry (MS/MS) scan for the fragment ions of eight TTXs arising from the molecular ions provided characteristic spectra, and the structures of the origins of the prominent fragment ions were proposed. The intense fragment ions of TTX and 11-deoxyTTX were applicable to LC/MS/MS operated in the selected reaction monitoring mode. This method might be useful for further identification of TTXs.