Kudoa septempunctata, a myxosporean parasite infecting the trunk muscles of olive flounder (Paralichthys olivaceus), has been recently reported to be the causative agent of a type of food poisoning in humans. Patients exhibited acute diarrhea and vomiting after ingestion of the raw flesh of infected flounder. A recent increase in the number of food-poisoning cases has prompted us to develop a control strategy of this parasite. In this study, we evaluated the efficacy of several temperature and chemical treatments for inactivating K. septempunctata spores in vitro using the vital staining assay with the fluorescent dyes Hoechst 33342 and propidium iodide (PI). Screening tests of treatment methods against K. septempunctata suggested that 25% ethanol for 5 min, 80°C for 10 s, limonene at 10 μL/mL for 5 min, and salinities at 0‰ and 160‰ for 5 min were effective for killing spores. To verify toxicity loss in K. septempunctata spores after the treatments, tight junction barrier integrity assays with Caco-2 cells were conducted. The results of the Caco-2 assays corresponded well with those of the Hoechst 33342-PI staining assay. Further studies are required to determine a practical treatment procedure for inactivating spores considering the treatment application in the production process of cultured olive flounder.