In the present study, we described a new species of Myxidium Bütschli, 1882, obtained from the gallbladder of Spinibarbus sinensis (Bleeker, 1871) from the Jialing River in Chongqing, China. Myxidium spinibarba sp. nov. was identified based on morphological and SSU rDNA sequence data. The mature myxospores were fusiform in valvular view and ovoid in sutural view, with somewhat protrusive poles and mean dimensions (all in μm) of 11.8 ± 0.5 (10.6-12.4) in length and 6.1 ± 0.5 (5.5-7.2) in width. The polar capsules were pyriform and equal in size with mean dimensions of 3.6 ± 0.4 (3.0-4.4) in length and 3.0 ± 0.2 (2.7-3.2) in width. The new species was distinct from related species of Myxidium in its morphology and molecular characteristics. Phylogenetic analysis indicated the clustering of species based on the presence or absence of valvular striations. Moreover, myxospore morphology, rather than the host environment, played an important role in the partial phylogenetic clustering.