The bull shark, Carcharhinus leucas, is an important euryhaline predator that is exploited throughout its range for meat and fins. This species is taxonomically paired with the pigeye shark, C. amboinensis. Validity of this group has not been directly tested using molecular markers. Genetic variation and phylogeny was examined with concatenated datasets of mitochondrial genes (cytb, cox1 and 12stRNA16s) for nineteen species, from three families within the order Carcharhiniformes. Whilst there were indications of species pairings within the genus, there was no evidence to suggest that the bull and pigeye sharks should be considered a species group. Phylogenetic analysis failed to resolve Carcharhinus, but confirmed Negaprion as a sister taxon and placed Prionace glauca within Carcharhinus. It remains unclear if the family Sphyrnidae, arose from a Rhizoprionodon or Scoliodon ancestor and future revision of this complex group of sharks is required. Like other large carcharhinid species, C. leucas exhibits a low reproductive rate and long generation times. It is susceptible to localised depletions and such declines have been documented. The global stock structure was assessed by analysing the mitochondrial control region in 245 individuals sampled from eight populations in three ocean basins. The bull shark exhibits relatively high haplotype diversity (0.896 ± 0.010) when compared to other globally-distributed sharks and the nucleotide diversity was similar to others from the genus (0.00465 ± 0.00014). There was significant stock structure found among populations (ΦST=0.736, p<0.00001) and among ocean basins (ΦCT=0.527, p=0.00653). Geneflow between the US Atlantic coastline and Gulf of Mexico was sufficient to consider the area to be a single panmictic population. Coalescent analyses suggest an Indian Ocean origin with population divergences associated with warm interglacials and increased habitat with drop in sea level during the recent Wisconsin glaciation. Seven discrete stock management units for bull sharks are proposed.