In the present study, we combined morphological and phylogenetic methods to characterize Myxobolus pseudonobilis n. sp. infecting Hypophthalmichthys molitrix Valenciennes, 1844 from Chongqing, China. The morphology and molecular characteristics of M. pseudonobilis n. sp. were distinct from those of other previously described Myxobolus species. Mature myxospores were ovoid in frontal view with spore dimensions of 10.0±0.4 (9.3-10.9) μm in length and 8.5±0.2 (7.9-9.0) μm in width. Two polar capsules occupying approximately half of the myxospore length were unequal in size. The larger polar capsule containing 6 to 7 filament coils measured 5.2±0.3 (4.5-5.8) μm in length and 3.6±0.2 (3.2-3.9) μm in width, while the smaller capsule with 4 to 5 filament coils measured 3.9±0.3 (3.0-4.4) μm in length and 2.5±0.3 (2.1-3.6) μm in width. The comparison of molecular characteristics demonstrated similarities and genetic distances of 18S rDNA sequences of 95.19% - 98.20% and 1.82% - 5.46%, respectively, between M. pseudonobilis n. sp. and its morphologically similar species, and secondary structures were also distinctly different. Moreover, phylogenetic analysis showed that M. pseudonobilis n. sp. was clustered with other myxobolids possessing spores with a blunt anterior end and branched independently. In addition, the morphology of myxosporeans as an important indicator was discussed.