The edible ascidian Halocynthia roretzi is a commercially important fisheries resource in Korea. However, for the last several years, outbreaks of mass mortalities of the species have been occurring along the south and east coasts of Korea, where most ascidians are produced. Although it is known that tunic-softness syndrome is associated with these mortality events, the agent causing the syndrome has not yet been confirmed. To determine the agent causing tunic-softness syndrome, healthy and diseased ascidians were collected in March 2011 from Tongyeong, on the south coast of Korea, and were used for biological and pathological investigations. The results showed that diseased ascidians exhibited remarkably reduced body fluid, fatness index, and tunic index compared with healthy specimens. Interestingly, bi-flagellated protozoans were observed specifically in the tissue imprints and tunic cultures of diseased ascidians at an occurrence rate of 97.5%. Histological observation showed that the thickness of the tunics of diseased ascidians was reduced by half, and irregular structure and breakdown of the tunic fiber bundles were observed. In particular, flagellate-like cells were observed in the diseased ascidians. Our study clearly shows that bi-flagellated protists are present only in the softened ascidians, suggesting that the flagellates are partly or entirely associated with soft-tunic syndrome. Accordingly, further investigations to verify the effects of the flagellates found in the present study on soft-tunic syndrome should be conducted.