Clestobothrium Lühe, 1899 is a genus of cestodes belonging to the order Bothriocephalidea, which infects marine fish from the Gadiformes order. Herein, a novel species of Clestobothrium is described from the intestine of the European hake Merluccius merluccius (Linnaeus, 1758) in the Ionian Sea (Eastern Mediterranean Sea), through an integrative taxonomic approach that combines morphological and molecular data. The new species, named Clestobothrium brettiae n. sp., can be distinguished from all congeners by its unique ovary shape, and a combination of characters including the arrangement and number of testes. It shares similar morphological characters, with Clestobothrium crassiceps (Rudolphi, 1819) Lühe, 1899, which overlaps in host and geographic distribution. However, morphological differences between Clestobothrium brettiae n. sp. and C. crassiceps also include the arrangement of gladiate spinitriches, as well as a larger scolex, proglottids, testes and cirrus sac, and different ovary morphology. The establishment of Clestobothrium brettiae n. sp. as a novel taxon is supported by detailed morphological description and biometric statistics, in addition to molecular characterisation (based on partial small subunit ribosomal ribonucleic acid [rRNA], partial large subunit rRNA, and internal transcribed spacer region 2), genetic distance, and phylogenetic analyses.