The Mediterranean and the Middle East represent unique biogeographical regions that significantly shaped the evolutionary history and particular diversity of their associated organisms. However, knowledge on the copepods parasitizing freshwater fishes in these regions is limited. This study aims to investigate the diversity and phylogeny of parasitic copepods in freshwater fishes across the Mediterranean and the Middle Eastern regions. A total of 169 freshwater fish species from the Mediterranean and Middle East were examined for metazoan parasites, yielding over 1000 parasitic copepods. A thorough morphological evaluation combined with molecular analyses of partial fragments of rDNA (18S and 28S) and mitochondrial cytochrome c oxidase subunit I (COI) led to the identification of 7 species of Ergasilidae and 3 species of Lernaeidae. These findings include the descriptions of 2 new species: Ergasilus italicus n. sp. parasitizing South European nase, Protochondrostoma genei (Bonaparte, 1839), in Italy and Pseudolamproglena zahrziensis n. sp. found in yellow barbel, Carasobarbus luteus (Heckel, 1843), in Iraq. New host and geographical records, along with molecular data are provided for 8 previously described species – Ergasilus barbi Rahemo, 1982, Ergasilus briani Markevich, 1933, Ergasilus lizae Krøyer, 1863, Ergasilus rostralis Ho, Jayarajan & Radhakrishnan 1992, Neoergasilus japonicus (Harada, 1930), Paraergasilus longidigitus Yin, 1954, Lamproglena pulchella von Nordmann, 1832 and Lernaea cyprinacea Linnaeus, 1758.