Harmful algal blooms are responsible for economic, societal, and health issues worldwide. In Japan, heterogeneity concerning diarrhetic shellfish poisoning (DSP) events has been reported, with most occurrences in the northern region. Although the toxin profile of Dinophysis cells from the DSP outbreaks has been investigated, no statistical comparison has been conducted on total toxin (particulate and released) production using cultured strains. A comparative toxin analysis was done based on >
400 strains of Dinophysis fortii from Japan's southwestern and northern areas to investigate the heterogeneity in toxicity. Regardless of the origin, the toxin profile of all strains was dominated by PTX2. However, OA was the second most abundant toxin in the southwestern and DTX1 in the northern strains. For DTX1, the average concentrations in the north (330.54 ± 223.03 ng/mL) were significantly higher than in the southwest (5.85 ± 8.92 ng/mL). PTX2 also displayed significantly higher average concentrations in the north (384.51 ± 240.03 ng/mL) than in the southwest (122.66 ± 125.1 ng/mL). However, the northern strains had significantly lower levels of OA (6.74 ng/mL ± 13.53) than those from the southwest (34.86 ± 38.47 ng/mL). The total toxin yield in the northern strain cultures was about 56 times higher for DTX1, whereas OA content was 5 times lower, indicating significant differences in toxic potential in the strains from the two regions. The results of this toxin analysis contribute to the explanation of the geographical differences in DSP outbreaks associated with the blooms of D. fortii in Japan.