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The hatchery-raised juveniles of Schizothorax wangchiachii, a species widely distributed in the Jinsha River and its tributaries in China, have shown improved swimming performance through exercise training. Understanding the underlying biological processes and molecular mechanisms responsible for this enhanced swimming ability is crucial. In this research, the transcriptome of muscle tissue was sequenced for juvenile S. wangchiachii subjected to exercise training. After thorough data processing, a total of 113,814 unigenes were obtained, with 57,500 of them annotated using various datasets including Pfam, GO, COG, Swiss-Prot, NR, and KEGG. The study identified 889 differentially expressed genes (DEGs) between the experimental and control groups after 30 days of exercise training, of which 439 were upregulated and 450 downregulated. Enrichment analysis highlighted that these DEGs were predominantly involved in molecular processes such as protein metabolism and breakdown, neurodevelopment, immunity, and growth and development. The expression patterns of the DEGs were validated through real-time PCR, corroborating the findings derived from transcriptome analysis. Further experimental investigation led to the recognition of MYLPF as a potential functional candidate gene for swimming ability in S. wangchiachii. The results provide novel insights into how S. wangchiachii adapts to exercise training, contributing to a deeper comprehension of the mechanisms that underlie exercise-induced improvements in fish swimming performance. [ABSTRACT FROM AUTHOR]