For the first time, Longicollum pagrosomi Yamaguti, 1935, an acanthocephalan parasite, has been characterized with morphological, histopathological and molecular detail in farmed red snapper (Lutjanus erythropterus) in Taiwan. The diseased fish showed clinical signs of anorexia, emaciation and were gasping for air at the water's surface. Gross examination revealed extensive necrosis in the intestine and even penetration at the site of parasitic attachment, resulting in a large number of parasites being lodged in the peritoneal cavity, surrounded by black hyperplastic connective tissue. The parasites collected from the intestine were studied using optical microscopy, histopathology, scanning electron microscopy (SEM) and molecular phylogenetic analysis. They were creamy white in colour, and were separated into their proboscis, neck and metasoma (trunk) under optical microscopy. Histopathological examination revealed ovarian balls (floating ovaries) inside the ligament sac and eggs within the egg sorting apparatus. The SEM images revealed that the proboscis had 11–14 longitudinal rows with 9–12 recurrent, backward‐facing, organized hooks. In the 18S and 28S phylogenetic tree, sequences of the specimens were identical to those of other Longicollum pagrosomi, in addition to the morphological features. Thus, we confirmed that the parasites belonged to Longicollum pagrosomi in this study.