The contents and composition of tetrodotoxin (TTX) and paralytic shellfish toxins (PSTs) in skin, muscle, and internal organs of two samples of marine puffer fish Canthigaster rivulata from Wakayama prefecture, Japan, were analyzed. Liquid chromatography-mass spectrometry (LC-MS) and high-performance liquid chromatography with post-column derivatization and fluorescence detection (LC-FLD) were used for the analysis of TTX and PSTs, respectively. For both samples, TTX and two analogues of PSTs, saxitoxin (STX) and decarbamoyl STX (dcSTX), were detected at levels over the limit of quantization (LOQ) only in the skin. These toxins in the muscle and internal organs were at trace levels, or not detected (ND). TTX contents were 11,000 and 13,000 ng/g (or 35 and 41 nmol/g), while PSTs contents were 168 and 460 ng/g (or 0.63 and 1.72 nmol/g) in the two skin specimens. The compositions of total toxin content were 98.2 and 96.0 mol% TTX and 1.8 and 4.0 mol% PSTs, respectively. Thus, the main contributor to toxin content in C. rivulata skin was TTX and the levels of PSTs toxicity in C. rivulata were very low. When the PSTs contents were converted into mouse unit score from the LC-FLD results, the resulting values of 1.0 and 2.8 MU/g of PSTs in C. rivulata skin were similar to those in Takifugu poecilonotus and Takifugu vermicularis in Japan, as determined in previous studies.