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During the cultivation of Marsupenaeus japonicus, there are often obvious differences in the growth within the same family under the same food, water quality, and environment, which greatly affects cultivation efficiency. To explore the molecular mechanism of this growth difference, this study used RNA-seq technology to compare the transcriptomes of M. japonicus individuals with significant growth differences from the same family. A total of 1375 differentially expressed genes were identified, of which 1109 were upregulated and 266 were downregulated. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed on the differentially expressed genes, and the results showed that growth-related processes, including chitin metabolism, chitin-binding amino sugar metabolism, and antioxidant processes, including response to oxidative stress, peroxidase activity, antioxidant activity, and peroxidase activity, showed significant differences between the large-size and small-size groups. The expression levels of some differentially expressed genes, such as cuticular protein, low-density lipoprotein receptor, ecdysteroid kinase, myosin heavy chain, and apoptosis inhibitor, were verified by quantitative PCR experiments. One cuticle gene was annotated, and phylogenetic analysis showed that this sequence clustered with the penaeid cuticle genes. This study provides valuable data and a scientific basis for understanding the mechanism of growth differences in M. japonicus at the molecular-genetic level. [ABSTRACT FROM AUTHOR]