The integrated use of a number of techniques that cover multiple aspects of a fish species' life history have been shown to provide the best basis for potential management of that species. Parasites provide information on aspects of short- to long-term aspects of a fish's biology, depending on the parasite species in question. In this study, the parasite fauna of three commercial and recreationally important fish species across northern Australia (Protonibea diacanthus, Lutjanus johnii and Lethrinus laticaudis) were examined in combination with microsatellite genetics and otolith microchemistry to determine potential stock structure for future management scenarios. A diverse range of parasites was found to infect all fish across the collection range from the Pilbara region in Western Australia to Moreton Bay in South-East Queensland. For all three fish species their parasite fauna provided high levels of reclassification success, usually 2-3x that calculated by chance alone, providing fine-scale spatial structuring of their fish hosts. Protonibea diacanthus had the highest level of reclassification success, with 67% overall, followed by Le. laticaudis with 56% and L. johnii with 44%. Once subdivided into jurisdictional management units, reclassification success increased with up to 90% of fish successfully reclassified in some regions. Between the three fish species, different groups of parasites were found to be better overall predictors of their host stock structure: encysted larval stages for P. diacanthus and L. johnii and external parasites for Le. laticaudis.