Myxobolus species represents a group of cosmopolitan metazoan parasites commonly harbored in the farmed and wild fish populations. Here, a species of Myxobolus is found in the kidney of an exotic mrigal Cirrhinus mrigala feral in the Yangtze River and utilized for an integrative characterization. Ellipsoidal myxospores are measured at 15.68 ± 0.8 (13.93-17.11) × 11.42 ± 0.54 (10.34-12.3) × 7.94 ± 0.35 (7.58-8.5) μm in dimension. The polar capsules are pyriform, and unequal in size. The morphological and morphometric characteristics of the present isolates are distinct from those of other congeners. Molecularly, the pairwise comparison based on the SSU rDNA sequence indicates that the present amplicon does not match any sequences available in the GenBank database and shares the highest similarity of 92.12% to Myxobolus pavlovskii (MG520369). Accordingly, we propose a name Myxobolus shuifuensis sp. n. for the present isolates. Phylogenetical trees indicate an apparent host-associated phylogenetic pattern. M. shuifuensis sp. n. groups loosely with other Myxobolus species isolated from Cirrhinus fish. Insead, it forms a sister clade to some myxosporeans belonging to the Thelohanellus genus. This result underpins the species identification and provides evidence for challenging the taxonomic separation among both morphologically comparable genera.