Despite increasing threats of extinction to Elasmobranchii (sharks and rays), whole genome-based conservation insights are lacking. Here, we present chromosome-level genome assemblies for the Critically Endangered great hammerhead () and the Endangered shortfin mako () sharks, with genetic diversity and historical demographic comparisons to other shark species. The great hammerhead exhibited low genetic variation, with 8.7\% of the 2.77 Gbp genome in runs of homozygosity (ROH) > 1 Mbp and 74.4\% in ROH >100 kbp. The 4.98 Gbp shortfin mako genome had considerably greater diversity and <1\% in ROH > 1 Mbp. Both these sharks experienced precipitous declines in effective population size (Ne) over the last 250 thousand years. While shortfin mako exhibited a large historical Ne that may have enabled the retention of higher genetic variation, the genomic data suggest a possibly more concerning picture for the great hammerhead, and a need for evaluation with additional individuals.