DNA barcoding refers to sequencing a short segment of DNA to identify samples to species level. Here, we present two cases in marlin from eastern Australia where DNA barcoding was required to resolve uncertainties in species identity. In Case 1, a recreational fisher caught an unusually small marlin (20 kg) consistent in size with black marlin (Istiompax indica) occurring in the region. However, this individual had the physical characteristics of a blue marlin (Makaira nigricans). DNA barcoding revealed that the small marlin was Makaira nigricans, the size of which has not been previously observed in eastern Australia. In Case 2, a partially digested billfish was found in a blue marlin stomach but could not be accurately identified to species. Whilst suspected to be a swordfish or other marlin species, DNA barcoding showed that the blue marlin had consumed an Indo-Pacific sailfish (Istiophorus platypterus). The size of this sailfish indicated that it was very young and may provide clues regarding sailfish spawning in the region. These cases demonstrate how resolving species identity with DNA barcoding can aid our understanding of the biology of marlin and other billfishes.