Gross and histological lesions caused by an intestinal parasite were described in three capybaras. The parasites presented a mean length of 14 mm and width of 7 mm, were round to oval or piriform, reddish and pedunculated, and adhered strongly to the mucosa of the large intestine. The intestinal mucosa at the parasite attachment site presented loss of surface epithelium and most glands, with replacement by fibrovascular proliferation that protruded from the mucosa and was involuted by the ventral sucker of the parasite. The lamina propria presented cellular debris, eosinophils, macrophages and plasma cells. The morphological characteristics, observed using serial histological sections, made it possible to classify the parasite as a trematode (Paramphistomatidae), compatible with Taxorchis schistocotyle. One capybara also harbored many ciliated protozoa in the large intestine (at the site of attachment of the parasite) and inside the caeca of the trematodes. In conclusion, this study described a multifocal necrotizing colitis associated with T. schistocotyle parasitism in capybaras.