Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays, and skates) and chimaeras, and the lack of established whole-genome sequence information for elasmobranchs has prevented our understanding of early vertebrate evolution and their unique phenotypic traits. Here we report whole genome sequencing and related molecular analysis of two elasmobranch shark species. Their genomes, whose sizes surpass that of ours, harbor sparse distribution of conserved genic and regulatory elements and exhibit reduced molecular evolutionary rates. Our investigation uncovered altered sensory gene repertory possibly associated with adaptation to unique underwater niche and relict members of the Hox C cluster previously hypothesized to be absent in elasmobranchs. We also showed the antiquity of gene repertory governing mammalian homeostasis and reproduction, including Leptin, by identifying their shark homologs. Our study provides the foundation of comprehensive exploration of morphology, physiology, and behavior of elasmobranch sharks at the molecular level, especially those with sustainable supply of animal samples.