Abstract: Myxosporea Bütschli, 1881 comprise a group of endoparasitic cnidarian with a two-host life cycle involving both an invertebrate definitive host and a vertebrate intermediate host. Myxidiidae Thélohan, 1892 demonstrates the broadest range of hosts among all myxosporeans. The species of which are typically coelozoic and rarely histozoic. Zschokklla Auerbach, 1910 represents the second most speciose genus in Myxidiidae, boasting over 100 nominal species. Zschokkella parasiluri Fujita, 1927 was first found in the gallbladder of Silurus asotus collected from Lake Biwa, Japan. Subsequently, this species was rediscovered in several locations, including Liaoning, Zhejiang and Sichuan in China, as well as in the USSR. However, due to the technological limitations of the time, molecular data on this species remained unavailable until recently. In this study, we obtained molecular data (18S rDNA) from two strains of Zschokkella parasiluri: one from Hubei (thereafter called Hubei strain, named S1 for short) and another from Yubei, Chongqing (thereafter called Chongqing Yubei strain, named S2 for short). In the present study, we obtained five geographical strains of the species from Shapingba in Chongqing (S3), Yubei in Chongqing (S4), Xiushan in Chongqing (S5), Tongren in Guizhou (S6) and Xinyang in Henan (S7). Xiushan, Tongren and Xinyang were the new geographical records of Z. parasiluri. While geographical isolation significantly impacts genetic divergence in free-living animals, the situation is more intricate for parasites, influenced by various factors. Surprisingly, limited research has been conducted in the field of Myxozoa. To explore the effect of geographical isolation on genetic divergence of Z. parasiluri strains, we conducted a comparative investigation based on morphological and molecular data. The results showed that the morphology of the five geographical strains of Z. parasiluri sampled in this study were basically consistent with the published strains. Specifically, mature myxopores of Z. parasiluri (S3) were oval with blunt ends, displaying 7—9 stripes in valvular view and wide spindle-shaped in sutural view. The suture line curved in an “S” shape and extend from one end to the other. Moreover, the mature myxospores measured 11.92±0.38 (11.15—12.60) μm in length and 6.28±0.50 (5.41—7.30) μm in width. Two polar capsules were spherical and equal in size located separately in the ends of the myxospores with 4.34±0.29 (3.76—4.84) μm in diameter and 6—7 turns of polar filaments. Principal component and significant difference analyses revealed no significant morphometric differences among the five geographical strains (S3—S7). The similarity of 18S rDNA sequence among 7 strains (S1—S7) ranged from 98.7% to 100%, and the genetic distance spanned from 0 to 0.006. The results indicated that there was a certain degree of genetic divergence among different geographical strains of Z. parasiluri. Phylogenetic analysis displayed no distinct clustering based on geographic origins, suggesting that geographical isolation might not be the crucial factor for the genetic divergence of Z. parasiluri strains. The analysis of sequence variation and secondary structure of 18S rRNA displayed that the Hubei strain (S1) was significantly different from those of other 6 strains (S2—S7), which indicated that though 7 strains of Z. parasiluri were at the level of intraspecific genetic variation, Hubei strain most probably have a distinct genetic origin. Since there was no morphological data available for the Hubei strain, the cryptic species of this strain could not be excluded, or the strain might be in the process of speciation of new species.