The scalloped hammerhead shark (Sphyrna lewini) is listed as a Critically Endangered species in the IUCN Red List and CITES appendix II. It's a coastal and semi-oceanic pelagic shark circumglobal in warm-temperate and tropical seas, from the surface and intertidal zone to depths of 1,043 m. The species is caught globally as a target and bycatch in pelagic commercial and small-scale longline, purse seine, and gillnet fisheries and is retained for the meat and fins. Sphyrna lewini has undergone steep declines in all ocean basins. The weighted global population trend estimated median reductions of 76.9–97.3%, with the highest probability of >80% reduction over three generation lengths (72.3 years). So, it is imperative to provide whole-genome sequencing data for the species aiming to aid and improve conservation efforts and sustainable fisheries management.