Several strains of Protoceratium reticulatum, one of the dinoflagellates producing yessotoxins (YTXs), were collected from various shellfish producing areas in Japan. YTXs in the cultured strains were analyzed by liquid chromatography-mass spectrometry (LC-MS). Neutral loss scan monitoring, multiple reaction monitoring (MRM) for more than 20 YTX analogues, and full-scan MS/MS spectra obtained with a hybrid triple quadrupole/linear ion trap mass spectrometer showed that yessotoxin (YTX), 45,46,47-trinoryessotoxin (trinorYTX), 1-homoyessotoxin (homoYTX), and 45,46,47-trinor-1-homoyessotoxin (trinor-1-homoYTX) were the dominant toxins in these strains of P. reticulatum. Enone isomer of 42,43,44,45,46,47,55-heptanor-41-oxoyessotoxin (noroxoYTX enone) was also detected in some strains. Toxin profiles and contents were different among the strains. Some strains produced YTX, trinorYTX, 1-homoYTX, trinor-1-homoYTX, and noroxoYTX enone, whereas other strains produced only YTX or 1-homoYTX. This is the first identification of 1-homoYTX and noroxoYTX enone in P. reticulutum in Japan. Some strains did not produce any detectable YTX analogues.