Abstract: Congjiang strain common carp (Cyprinus carpio, CJ), accustomed to the GIAHS in Congjiang County, Qiandongnan Miao and Dong Autonomous Region, Guizhou Province of China, is suitable for living in shallow water bodies in paddy field due to its less locomotion behavior (local nickname “dull carp”). While the FFRC No. 2 strain common carp (FR), a nationally authorized improved aquaculture variety (registration number GS-01-003-2017) for high growth rate and survival rate, has more active locomotion behavior, resulting in a high escape potential when cultured in paddy fields. In order to explore the functions of ube3a and myomaker genes in muscle fiber development and motility differences between FR and CJ, the RACE technology was applied to clone the full-length cDNA of ube3a and myomaker genes. The properties of their encoding proteins were analyzed. The expression patterns of the two genes were explored by Real-time fluorescence quantitative PCR analysis and location information of the two genes were detected by in situ hybridization. Finally, the functions of ube3a and myomaker genes involved in the regulation of muscle fiber development were discussed. The results showed that ube3a in both common carp strains encoded 857 amino acids and contained a HECT domain. The myomaker gene in FR encoded 220 amino acids, while in CJ it encoded 259 amino acids. The CJ Myomaker protein contained a CNMP (cyclic nucleotide monophosphate-binding domain) domain. Expression analysis revealed that the transcript level of ube3a and myomaker was both significantly higher in CJ muscle compared to FR (P< 0.05). In situ hybridization results indicated that ube3a was localized in both the nucleus and cytoplasm of muscle fibers, whereas myomaker was mainly located on the cell membrane of muscle fibers. In conclusion, we speculate that the reason for the low motility ability of CJ may be that the high expression of ube3a in muscle causes the high degradation of muscle fiber protein, and the CNMP structure of myomaker gene, which may regulate the environmental adaptation, affect the fusion efficacy of myomaker function. Our findings provided a molecular basis for understanding motility differences in fish and reference for further elucidation of the regulatory mechanisms underlying muscle fiber development.