The great hammerhead shark, Sphyrna mokarran, is a circumglobal coastal-pelagic species of high conservation concern (IUCN Red List: Endangered). Our earlier analysis of mitochondrial control region sequences in globally distributed animals uncovered two highly genetically divergent matrilines in this species (Testerman et al. In prep.). Here we present findings of a genomic level assessment of global population dynamics of the great hammerhead shark based on analyses of nuclear single nucleotide polymorphisms (SNPs) and whole mitochondrial genome sequences (17,719 bp). Analysis of 2330 neutral SNP loci with Discriminant Analysis of Principal Components (DAPC) and the Bayesian clustering program STRUCTURE reveals three geographic meta-populations (Western Atlantic, North Indian Ocean, and Australia). Pairwise comparisons (FST, G’’ST, and Jost’s D) further reveals highly structured sub-populations within these regions including evidence of differentiation between Western Australia and Eastern Australia individuals, which was previously undetected. Analysis of molecular variance (AMOVA, FST) of whole mitochondrial genomes supports the three meta-populations, with a lesser degree but still significant level of sub-population structuring. A median joining haplotype network additionally supports the previously detected divergent matrilines, separated by an estimated 99 mutational steps. Preliminary demographic analyses support the hypothesis of an Indo-West Pacific origin followed by colonization of the Indian Ocean and subsequently the Atlantic.