One specimen of John Dory, Zeus faber (Linnaeus, 1758), was caught from commercial sites at the costs of Gulf of Antalya at Mediterranean Sea, Turkey. Zeus faber was dissected carefully. After examination Anisakidae larvae were recovered from in the abdominal cavity, liver and muscles. A total of eight larvae were found in the abdominal cavity and seven larvae encapsulated on surface of liver at necropsy. In the macroscopic examination, liver was seen to pale and surface of the capsula was haemorhagic with subcapsular cysts including larvae in 0.3 cm diameter. In the histopathologic examination severe degeneration and hepatic necrosis was identified. Just below the liver capsula, Anisakis larvae were seen covered with fibrous capsula. The larvae morphologically identified as Anisakis larvae Type I were subjected to further molecular characterization by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to identify the species. All Anisakis larvae were identified at species level by PCR-RFLP as belonging to A. pegreffii. Within the present study, for the first time, we report on the molecular identification of A. pegreffii larvae from John Dory, Z. faber, and we describe their pathological significance in a paratenic or intermediate hosts in Turkish waters.