BackgroundMyxozoans are a group of cnidarian parasites, the present taxonomy of which favors a more comprehensive characterization strategy combining spore morphology, biological traits (host/organ specificity, tissue tropism), and DNA data over the classical morphology-based taxonomy. However, a systematist might again run into a taxonomic dilemma if more than two of the following exceptional cases were encountered at the same time: extensive intraspecific polymorphism, interspecific morphological similarity, identical interspecific biological traits and blurred small-subunit (SSU) rDNA-based species boundaries. In the present study, spores of a species of Myxobolus Bütschli, 1882 with two morphotypes (wide type and narrow type) were collected from the gills of common carp Cyprinus carpio Linnaeus. Confusingly, the wide type was found to be identical to Myxobolus paratoyamai Kato, Kasai, Tomochi, Li & Sato, 2017 in spore morphology and SSU rDNA sequence, which confidently suggested their conspecificity; while the narrow type, was highly similar to Myxobolus toyamai Kudo, 1917 based on spore morphology and SSU rDNA sequence and thus could not be easily classified. This discordance between wide type and narrow type has caused a taxonomic dilemma. To address this problem, a hypothesis about the conspecificity of the narrow type and M. toyamai was addressed.ResultsIt was found that if the narrow type is conspecific with M. toyamai, it would be paradoxical for the SSU rDNA sequence of the narrow type to be more similar to M. paratoyamai (99.3%), Myxobolus acinosus Nie & Li, 1973 (98.6%) and Myxobolus longisporus Nie & Li, 1992 (98.7%) than to M. toyamai (97.6%). According to the results of the above what-if analysis, the narrow type and M. toyamai were considered to be different species. All in all, the present dual-morphotype species is estimated to be conspecific with M. paratoyamai Kato, Kasai, Tomochi, Li & Sato, 2017. Considering that this species name was preoccupied by Myxobolus paratoyamai Nie & Li, 1992, the replacement name Myxobolus pseudoacinosus nom. nov. is proposed.ConclusionsThis work addresses the taxonomic dilemma in polymorphic myxozoans and demonstrates that M. pseudoacinosus is a distinct species with two morphotypes. The present study may serve as a baseline for future studies that encounter similar classification complexities.Electronic supplementary materialThe online version of this article (10.1186/s13071-018-2943-0) contains supplementary material, which is available to authorized users.