Abstract: Amusium japonicum is an important economic scallop species in China, and there has been a long-term phenomenon of homonym. In this study, the morphology of A. japonicum was studied using traditional morphological, molecular biological, and geometric morphological methods. The study aimed to identify the differences between A. japonicum and similar species and re-describe and revise its taxonomic classification in the South China Sea, thereby contributing to scallop taxonomy and phylogenetics research. The results indicated that A. japonicum occupied a distinct phylogenetic position relative to A. pleuronectes. and the taxonomic status of Chinese A. japonicum was corrected for the first time, from the genus Amusium into a newly established genus Ylistrum, with the updated scientific name Ylistrum japonicum. A maximum likelihood phylogenetic tree clearly separated Y. japonicum from A. pleuronectes, highlighting their divergent evolutionary lineages. There are 34—52 inner ribs in the left shell of Y. japonicum, with an average of 40, and 43—55 in the right shell, with an average of 47, and Y. japonicum is gonochorism. There are 22—30 internal ribs in the left shell of the A. pleuronectes, with an average of 25, and 22—30 in the right shell, with an average of 26, androgynous. According to divergence time estimation, the divergence time of the Y. japonicum is approximately 108.47 million years ago (Mya), corresponding to the early Cretaceous period of the Mesozoic era.