This study analyzed the differential gene expression in the muscle of Litopenaeus vannamei with different growth rates caused by dietary fish (FO) or canola oil (CO) in feed to expand the knowledge of how a low n-3 highly unsaturated fatty acids (HUFA) diet affects growth performance. As expected, after a 28-day feeding trial, juvenile L. vannamei fed FO showed significantly higher final weight, weight gain, and specific growth rate than those fed CO. Furthermore, the muscle tissue in FO shrimp showed higher levels of eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3) compared to CO shrimp. Transcriptional sequencing analysis on the tail muscle identified 98 genes expressed differentially between both treatments, mainly expression on myosin and actin isoforms related to growth rates. Moreover, shrimp fed with FO presented upregulated genes related to higher metabolic activity associated with enhanced growth rate. Shrimp fed CO had downregulation of genes associated with energy metabolism, potentially related to lower energy demand for growth. These findings enhance the comprehension of the relationship among diet composition, gene expression, and shrimp growth under culture conditions. Furthermore, the determination of selected gene expression like those found in the present study could be a potential tool to identify a cause of low shrimp growth in farms caused by a deficient HUFA diet.