The interplay between genetic and environmental regulation in biological development and evolution represents a central theme ecology and genetics. In marine ecosystems, temperature, as a critical ecological driver of climate change, exerts profound regulatory effects on migratory patterns and distribution dynamics of marine fishes, significantly shaping their evolutionary potential. Investigating the genetic mechanisms underlying regional endothermy and thermal adaptation in fishes is essential for elucidating evolutionary and developmental regulation while advancing species conservation efforts. This review synthesizes the phylogenetic relationships of regionally endothermic fishes and examines the structural characteristics of thermogenic tissues (e.g., red muscle, visceral organs, brain, and cranial specialized heater tissues) and associated counter-current heat exchange vascular networks. From molecular and physiological perspectives, we elucidate the mechanisms of heat production in regional endothermy and critically evaluate potential drivers of its evolution. Our findings provide critical insights into the adaptive responses of fishes to climate change and deepen the understanding of convergent evolution in vertebrate thermoregulatory strategies. This work underscores the importance of integrating genetic, physiological, and ecological approaches to unravel the complexities of thermal adaptation in marine systems.