Abstract: Myxozoans are important parasitic pathogens of koi carp. In the present study, a Myxobolus species was found to infect gills of koi carp Cyprinus carpio koi. In order to identify this Myxobolus species, it was comprehensively described by morphological, histological and molecular methods, and its phylogenetic relationship was inferred as well. We found that the present Myxobolus species infected the gills of koi carp and formed a number of white plasmodia in all gills. Compared with all reported Myxobolus species, the present Myxobolus species was morphologically indistinguishable from M. acinosus. Histological analysis showed that the plasmodia of the present Myxobolus species developed in gill lamella of host, causing significant epithelial cell proliferation and congestion in the gills. Its parasitic characteristics are consistent with those of M. acinosus. BLAST search showed that SSU rDNA sequence of the present Myxobolus species was identical to M. acinosus (Accession numbers: KX810021–KX810022, MW821466–MW821468). Thus, the morphological, histological and molecular analysis demonstrated that the present Myxobolus species was conspecific with M. acinosus. Phylogenetic analysis revealed that the majority of myxozoans infecting the same host and organ formed independent lineages. However, myxozoans infecting different hosts and the same organ formed larger independent branches, indicating that sites of infection provide a stronger driving force for the evolution of myxozoans compared to host group.