The present study is the first morphological and molecular characterization of a monogenean Eudiplozoon nipponicum (Goto, 1891) parasitizing gill filaments of common carps (Cyprinus carpio) obtained from the Lesser Zab River in northeastern Iraq in the subdistrict of Altun-Kopru from July to October 2022 and transported to the Laboratory of Zoology Research, Salahaddin University-Erbil, Iraq. Most previous studies regarding the considered parasite have targeted morphological data analysis. However, DNA sequence outline is typically supportive in systematics, since it contains aspects that are absent from morphological research. The main goal was to molecularly identify E. nipponicum utilizing the nuclear 28S rDNA region by PCR and nucleotide sequencing approach. The sequences were obtained and compared to the accessible GenBank sequences. The results justify the validation of E. nipponicum in Iraq using traditional (morphology-based) and modern (molecular-based) parasitological techniques. The latter one showed 99.11% (identity percentage) of E. nipponicum in comparison to the registered sequences of NCBI. Additionally, this was considered the first wide-ranging morphological and molecular study in the studied region. The phylogenetic relationship was concluded using Maximum Likelihood (ML) method. It was concluded that besides of the morphological characterization of E. nipponicum, PCR sequencing was considered a suitable molecular method for recognizing monogenean diplozoid species on the fishes.