Myostatin (MSTN), a member of the transforming growth factor-β superfamily, negatively regulates skeletal muscle growth in vertebrates. In teleosts, gene duplication has produced mstn1 and mstn2 paralogues, which often differ in structure and expression. This study compares mstn1 and mstn2 in two high-value mariculture-relevant carangids of the Indo-Pacific region, Trachinotus mookalee and Trachinotus blochii. We report, for the first time, the complete gene structures of mstn1 and mstn2 in T. mookalee (3777 bp from Tm-mstn1 and 2075 bp from Tm-mstn2) and describe their counterparts in T. blochii (3836 bp from Tb-mstn1 and 2147 bp from Tb-mstn2). Notably, mstn1 and mstn2 shared only ∼53% sequence identity within the same species. Interestingly, we noted a CA-repeat tandem sequence in intron 2 (35 bp in Tm-mstn1 and 47 bp in Tb-mstn1), providing a potential microsatellite marker. Promoter analysis suggested more complex transcriptional regulation in T. blochii, with a greater number of transcription factor binding sites (47 vs. 43) and E-box motifs (4 vs. 2). Predicted miRNA binding site revealed both shared (14) and species-specific sites (two sites in Tm-mstn1, and one in Tb-mstn1), indicating differential post-transcriptional regulation. These molecular differences were verified through differential mstn1 expression, with higher mstn1 expression in T. blochii muscle, which might be the reason for the enhanced muscle growth in T. mookalee. The mstn2 expression patterns supported its role in neuroendocrine and reproductive regulation. Overall, this study provides new molecular insights into species-specific growth differences and highlights the functional divergence of mstn genes in marine carangids.