Purpose Describe a new species of didymozoid digenean Neonematobothrium Yamaguti, 1965 from the operculum of the scombrid fish, Euthynnus alletteratus (Rafinesque, 1810), in the Southwest Atlantic Ocean off Brazil. Methods Thirty-four specimens of E. alletteratus were collected in the coastal zone of the state of Rio de Janeiro and obtained from local fishermen between 2006 and 2018 in the municipal market of São Pedro in Niterói, Brazil. The parasites were fixed in AFA (93% ethanol 70%, 5% formaldehyde, 2% glacial acetic acid) without pressure, stained with Langeron alcoholic acid carmine, dehydrated in an alcohol series, cleared in beachwood creosote or clove oil and mounted in Canada balsam as permanent slides. Results Neonematobothrium annakohnae n. sp. is a member of the genus based on a combination of the following characteristics: body free, uncapsulated; body long and dorsoventrally flattened; esophagus surrounded by gland cells; ovary and vitellarium single, long, narrow and unbranched in the anterior and posterior halves of the body, respectively; uterus with three loops; and site of infection in subcutaneous tissue of scombrid fish. The new species differs from the two recognized species of the genus mainly by the size of the body, which is much larger, the shape of the genital pore, which is differentiated in a structure similar to a small sucker and by esophagus without diverticula. Conclusions Neonematobothrium annakohnae n. sp. parasite of E. alletteratus from the Southwest Atlantic Ocean, described herein, represents the third species of Didymozoidae belonging to the genus Neonematobothrium. The two known species Neonematobothrium kawakawa Yamaguti, 1965 and Neonematobothrium dorsale Yamaguti, 1970 were described from fish belonging to the same genus of the host from Pacific Ocean. The diagnosis of the genus is enlarged to “esophagus with or without diverticula”, to fill the characteristics presented by the new species. The description of N. annakohnae n. sp. demonstrates the need to expand the studies of these interesting and intriguing group of parasites, due to the fact that number of known didymozoids taxa in the Atlantic Ocean is far from representing the real situation.