Abstract: Thelohanellus wuhanensis Xiao & Chen, 1993, a pathogen of "skin myxosporidiosis", infects the skin of gibel carp Carassius auratus gibelio, and can cause significant mortality in juvenile fish. Researche on T. wuhanensis has primarily focused on its identification, pathogenicity,and life cycle, with little attention has been paid to the potential bacterial secondary infections it may cause. Here, the skin microbiota analysis (including the species diversity, composition, and abundance) of Carassius auratus gibelio infected by T. wuhanensis were conducted using high-throughput 16S rDNA sequencing. The results indicated that both the healthy and infected groups of C. auratus gibelio possessed a total of 30 phyla, 80 classes, 188 orders, 295 families, 475 genera, 692species, and 939 OTUs (Operational Taxonomic Units). The healthy group had 308 unique OTUs, while the infected group had 342 unique OTUs. The α-diversity analysis revealed significantly higher microbial diversity but significantly lower richness in the infected group compared with the healthy group. Furthermore, the β-diversity analysis demonstrated significant differences in the structure of skin microbial communities between the healthy and infected groups. At the phylum level, Firmicutes, Proteobacteria, Cyanobacteria, Actinobacteria, and Bacteroidetes were the dominant taxa in both the healthy and infected groups, although differences in abundance were observed. At the genus level, 20 genera exhibited a relative abundance exceeding 1%. The dominant genus in the healthy group was Lactococcus, while Achromobacter was the most prevalent in the infected group, representing 58.99% and 48.67% of the total microbial abundance, respectively. The results of the LDA (linear discriminant analysis) and functional prediction indicated a significant increase in both the abundance of pathogenic bacteria and the potential pathogenicity of the microbiota in the infected group in comparison to the healthy group. In conclusion, the infection of T. wuhanensis can disrupt the skin microbiota of C. auratus gibelio, increase the abundance of pathogenic bacteria, and potentially promote the invasion of pathogens.