Abstract: Microsatellites are efficient and stable genetic markers widely used in the constructing genetic maps, identifying genetic relationships, and analyzing population genetic diversity. However, there is no information on microsatellites in the genome of myxosporean. In this study, we investigated the characteristics and distribution patterns of microsatellites in the whole genome of Myxobolus episquamalis, the pathogen of mullet lepriasis. The total number of complete microsatellites was 21957, with a combined length of 311751 bp, constituting 0.3% of the whole genome size. Among the six microsatellite repeat types, single-base-repeat type had the largest number, accounting for 42.5%, followed by two-bases-repeat type (26%), three-bases-repeat type (17.9%), four-bases-repeat type (12.5%), five-bases-repeat type (0.8%), and six-bases-repeat type (0.4%). Additionally, 93 microsatellites were located in exons corresponding to 39 genes. GO analysis of these genes showed that the most were annotated to biological processes, with the most significant entries being intracellular and organellar components. KEGG analysis showed that these 39 genes were involved in 80 pathways, in which the collecting duct acid secretion pathway was the most significant. The characteristics and distribution patterns of microsatellites in the M. episquamalis genome were most similar to those in Cnidaria, which provided a new evidence supporting the hypothesis that myxosprean originated from Cnidaria. Microsatellites localized in exons may be closely associated with biological metabolic processes in vivo. Our study first acquired the characteristics and distribution patterns of microsatellites of myxosporean, which could provide a valuable reference for developing microsatellite markers and conducting genetic analysis of myxosporean. This knowledge could also aid in the prevention and control of myxosporidiosis.