Pseudorhabdosynochus seabassi sp. n. (Monogenea: Diplectanidae) from the gill filaments of Lates calcarifer Bloch, a marine teleost fish held in floating sea cages in Guangdong Province, China, is described based on morphological observations and molecular data. The shapes of the male copulatory organs (MCO) of Pseudorhabdosynochus spp. were the focus of this study. The typical proximal part of the MCO in most species of Pseudorhabdosynochus is reniform, heavily sclerotized, and divided into four chambers. However, the new species from L. calcarifer has a bulbous proximal region with four concentric layers of apparent muscular origin, instead of a reniform structure with four compartments. This organ is also different in Diplectanum grouperi Bu, Leong, Wong, Woo et Foo, 1999, being sclerotized, cup-shaped, wide proximally with four concentric muscular layers and tubular distally. The 3' terminal portion of the small subunit ribosomal RNA gene (ssrDNA) and the 5' terminal region (domains C1-D2) of the large subunit ribosomal RNA gene (lsrDNA) were used to reconstruct the phylogenetic relationships of P. seabassi and D. grouperi with related taxa utilizing maximum-parsimony and neighbour-joining methods. Phylogenetic analyses unequivocally placed D. grouperi amongst Pseudorhabdosynochus using either ssrDNA or lsrDNA data. All species of Pseudorhabdosynochus (including D. grouperi) used in this study clustered together, inferring monophyly. Based on molecular phylogenetic evidence, we propose that D. grouperi from Epinephelus coioides Hamilton be transferred to Pseudorhabdosynochus as P. grouperi comb. n.