Abstract: Parasites were observed during land-based farming of the small tuna (Euthynnus affinis) in Tropical Fisheries Research and Development Center, Sanya, Hainan. In this study, the parasite was isolated and morphologically observed, and 18S and 28S rRNA molecules were identified. The 18S rRNA showed 99.12% similarity to Branchiomma sp. (EF116223.1) and 28S rRNA showed 100% similarity to B. nigromaculatum. The parasite was found on the surface of the posterior margin of gill arch and middle and posterior part of pectoral fin of E. affinis. The body of the worm was dark green, brownish yellow or reddish brown, with a gill crown, and the total length was 30–90 mm. The parasite consisted of gill crown, chest and abdomen, but calcareous canal was not found. Its digestive tract included mouth, pharynx, intestine and anus. Therefore, the parasite might belong to Branchiomma and B. nigromaculatum, but further verification is needed. The infected fish reduced food intake significantly, accelerated the swimming speed, and were easily frightened. Formalin immersion had a good removal effect, and the survival rate of the fish after cure was 75.9%.