Pelagic cephalopods have evolved a series of fascinating traits, such as excellent visual acuity, high-speed agility, andphotophoresfor adaptation to open pelagic oceans. However, the genetic mechanisms underpinning these traits are not well understood. Thus, in this study, we obtained high-qualitygenomesof two purplebackflying squidspecies (Sthenoteuthis oualaniensisandSthenoteuthissp.), with sizes of 5450 Mb and 5651 Mb, respectively. Comparative genomic analyses revealed that theS-crystallin subfamilySL20-1associated with visual acuity in the purpleback flying squid lineage was significantly expanded, and theevolutionof high-speed agility for the species was accompanied by significant positive selection pressure on genes related to energy metabolism. These molecular signals might have contributed to the evolution of their adaptative predatory and anti-predatory traits. In addition, the transcriptomic analysis provided clear indications of the evolution of the photophores of purpleback flying squids, especially the recruitment of new genes and energy metabolism-related genes which may have played key functional roles in the process.