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In this study, we identified the important contribution of frontal bone remodeling in shaping the ‘sunken head and humpback’ appearance in <i>C. altivelis</i>. Our investigation identified a developmental milestone at a total length of 5–6 cm, making the onset of its morphologic specialization in this species. A comparative analysis with closely related species reveals heightened activity in the frontal osteoblasts of the humpback grouper, potentially providing a physiological basis for its remodeling. Furthermore, our findings highlight that a significant upregulation in the expression levels of <i>Ihhb</i>, <i>Ptch1</i>, and <i>Gli2a</i> genes was seen in <i>C. altivelis</i> within the specified developmental stage, indicating an important involvement of the <i>Ihhb</i>-<i>Ptch1</i>-<i>Gli2a</i> signaling pathway in initiating the morphological specialization. We hypothesized that Ihh signaling could be attributed to shifts in mechanical stress, resulting from muscle traction on the frontal bone due to changes in swimming patterns during development. This study not only offers significant insights into unraveling the molecular mechanisms that govern phenotypic specialization and ecological adaptations in the humpback grouper but also serves as a valuable reference for studies on fishes with a controversial morphology and molecular phylogeny.