Data collected by fisheries observers are important for effective fisheries management. With large, multi-species fisheries often catching a diverse range of species, the accurate identification of morphologically similar species represents an ongoing challenge. High levels of misidentification and misreporting of catch at the species level has been previously identified to influence the information that is used to determine the status of billfish. In this study, we investigated whether commercially landed black marlin were being misidentified by fisheries observers operating throughout the Pacific Ocean. Observed records of landed catch were compared to samples from those fish by genotyping across a suite of microsatellite markers. Genetic assignment testing revealed that, of 83 samples reported by observers as black marlin, 77.1% were genetically identified to be blue marlin and 2.4% to be striped marlin. The high rate of misidentification by observers places considerable uncertainty over historic catch ratios of Indo-Pacific marlin and stock assessments relying on the validity of these data.