The black marlin, Istiompax indica,is a pelagic species whose distribution ranges throughout the tropical and subtropical waters of the Indo-pacific. The IUCN Red List of Threatened Species defines I. indica as ‘data deficient’ due to a lack of information on the population structure of this species. For the purpose of resolving the population structure of I. indica 18 polymorphic microsatellite loci were isolated and characterised from Next-Generation sequencing data. The mitochondrial control region and panel of 18 microsatellite loci were used to analyse 205 young-of-the-year black marlin samples collected by non-lethal sampling in catch and release recreational fisheries. The sampling sites comprised five indo-pacific regions (East Indian Ocean, West Pacific Ocean, North Tasman Sea, South China Sea and the Gulf of Carpentaria), which were identified as representing ocean basins or regions of inter-oceanic connectivity. Parsimony network analysis of the control region sequences suggested the presence of genetic admixture, distinguishing three distinct clades which were not concordant to geographic locality. Investigation of the microsatellite loci revealed the presence of significant structure throughout the range which conforms with the species’ biogeography. The pronounced signatures in the mitochondrial clades may reflect ancient subdivision during times of sea level fluctuation, followed by periods of admixture. A comparison of the mito-nuclear markers suggests the presence of discordance.