The family Unionidae is a diverse and ecologically significant group of freshwater invertebrates, playing a keystone role in the energy flow and nutrient cycling in aquatic ecosystems. A recent taxonomic revision of the East Asian endemic subtribe Cristariina within Unionidae has revealed its division into seven genera. As an important part of East Asia, China harbours an exceptionally diverse and highly unique fauna of freshwater mussels. However, a comprehensive understanding of species diversity and phylogenetic relationships of Cristariina remains elusive due to inadequate sampling in previous studies, particularly in China. Here, we conducted comprehensive taxonomic and mitogenomic phylogenetic analyses of Cristariina based on extensive sampling across 17 provinces in China. The COI sequences of Cristariina in GenBank were thoroughly examined, and combined with the sequences obtained from this study, a total of 33 monophyletic groups were identified. By integrating molecular data and morphological characteristics, we describe a new genus and species: Acudonta baitiaoensisgen. nov., sp. nov., as well as a newly recorded species for China (Cristaria truncata). Additionally, we confirm that the nominal species Anemina euscaphyssyn. nov., Anemina flumineasyn. nov. and Anemina globosulasyn. nov. are junior synonyms of Anemina arcaeformis through integrative taxonomy. Mitogenomic phylogeny establishes the following robust phylogenetic framework at the generic level within Cristariina: ((((Sinanodonta + Acudontagen. nov.) + (Beringiana + Pletholophus)) + ((Anemina + Buldowskia) + Amuranodonta)) + Cristaria). Besides Sinanodonta and Cristaria, the distribution of other genera of Cristariina in China exhibits distinct faunal regions of endemism. ZooBank: urn:lsid:zoobank.org:pub:30E44DEB-3CCD-47F7-A2B2-3FA851BE434E