Tissue encapsulation, one of the most common tissue reactions to invading parasites, is the hallmark sign of didymozoid (Digenea, Didymozoidae) infections in fish. Investigated were the types of intermediate filaments and ultrastructure of the connective tissue capsule elicited by the presence of didymozoids in the gills and intestine of Atlantic bluefin tuna (Thunnus thynnus Linnaeus, 1758). The evaluation was done performing TEM microscopy of two tissue-embedded didymozoid species, along with monoclonal antibodies labeling (anti-fish collagen type I, anti-human cytokeratin, anti-vimentin antibodies). Ultrastructure of Didymocystis wedli (Ariola, 1902) (prevalence = 61.75%, abundance = 28.91) encapsulated in gill filaments and Koellikerioides intestinalis (Yamaguti, 1970) (prevalence = 54.65%, abundance = 10.96) in the intestinal submucosa showed that the thin parasitic hindbody tegumentum was directly embedded in layers of connective tissue bands. Only a few cellular elements (lymphocytes, fibroblasts and fibrocytes) infiltrated the connective tissue capsule, which differed between the two didymozoid species in thickness, not in the type of filaments expressed. Cysts showed positive reaction to extracellular collagen as well as appearing positive for the cytoskeletal intermediate filaments vimentin and cytokeratin.