Objectives The parasites in the cases of Apostichopus japonicus were isolated and identified, and its pathogenic factors were analyzed to provide a reference for the diagnosis, prevention and control of scuticociliate in A.japonicus. Methods Microscopic examination was conducted on the epidermis, body wall, muscles, body cavity fluid, respiratory tree, and intestines of the A.japonicus sent from a farm in Liaoning Province for inspection. The observed ciliates were cultured in vitro and its 18S rDNA were sequenced. Results The ciliate H-1, H-2, H-3 and H-4 was observed in various tissues and organs of the diseased ginseng. The ciliate H-4 was identified as a Boveria Stevens based on morphology. The ciliate H-3 and H-5 not observed under microscopy were successfully cultured in vitro. The alignment of the 18S rDNA sequences of ciliates H-3 and H-5 showed that they were U.marinum. Conclusions In this case, various scuticociliate were parasitized in the tissues of A.japonicus, while U.marinum were parasitized in the body cavity fluid, and Boveria Stevens and U.marinum were parasitized in the respiratory trees.