Kudoa septempunctata is a myxosporean parasite of Paralichthys olivaceus (olive flounder) that causes more than 50 cases of foodborne illness in Japan each year. For quantitatively assessing the presence of K. septempunctata spores in the causative fish at food poisoning outbreaks, both a direct observation method using microscopy and a quantitative real-time PCR (qRT-PCR) method are officially accepted in Japan. However, lower correlations have been often noticed between the number of spores counted using the direct observation method and the DNA amount determined using the qRT-PCR method. To elucidate the cause of this discrepancy, we observed muscle tissues of infected olive flounders with K. septempunctata by transmission electron microscopy. The images demonstrated unsynchronized development of K. septempunctata spores in plasmodia found within myofibers; in other words, the plasmodium contained not only developed spores with completed shell valves but also developing spores (sporoblasts) composed of spore-forming cells without shell valves. Furthermore, the ratio between developed spores and sporoblasts varied at different parts of muscles. The direct microscopic observation method could count developed spores, whereas the qRT-PCR method could quantify the amount of not only spores but also sporoblastic cells regardless of the cellular development and differentiation. Considering that the food toxicity caused by K. septempunctata is induced by viable spores passing through the gastric environment, the direct observation method counting only developed spores is better than the qRT-PCR method for assessing the cause of foodborne illness at the outbreak as well as the risk of human illness in monitoring surveys of aquacultured or natural-water fish.