Empruthotrema chisholmae n. sp. is described from specimens recovered from a bull ray Pteromylaeus bovinus (Geoffroy Saint-Hilaire, 1817) at the Oceanogràfic Aquarium in Valencia, Spain. The bull ray was caught in the Spanish Mediterranean (Puerto de Mazarrón, Murcia). The new species resembles 4 others of the same genus (Empruthotrema dasyatidis Whittington and Kearn, 1992, Empruthotrema kearni Whittington, 1990, Empruthotrema stenophallus Chisholm and Whittington, 2005, and Empruthotrema tasmaniensis Chisholm and Whittington, 1999) in having a haptor with 13 marginal loculi, the posteriormost loculus single and medial. The new species can be distinguished from these other species of the genus by the morphology of the sclerotized male copulatory organ, which is the shortest described. The new species also differs from the other species by the following combination of features: haptor with 13 marginal loculi, the presence of eyespots, the absence of an accessory piece associated with the male copulatory organ, and a long egg appendage (more than 150 µm). Empruthotrema chisholmae is the first species of the genus reported from the Mediterranean.