The eastern king prawn, Penaeus (Melicertus) plebejus, is widely distributed along the east coast of Australia. It exhibits great mobility and the species distribution transcends management jurisdictions of the three eastern states. The species is targeted for stock enhancement, which requires managers to avoid genetic loss in aquaculture, or using inappropriate stock in restocking.  Highly variable mitochondrial control region (mtCR) was used to examine the reproductive performance of wild-caught female broodstock in the production of hatchery-bred cohorts for restocking. Our data showed that mtCR can be a useful tool for tracking lineages and provided clear genetic evidence that unequal contribution and under-producing females can be common even in wild-caught broodstock, therefore highlighting the importance of monitoring the genetic composition of hatchery cohorts prior to release for stock enhancement. Also, using kinship verified by hatchery observations and mtCR haplotypes, we showed that microsatellite null alleles are very common.  We compared several methods of microsatellite allele estimation; pedigree-free and pedigree-based methods provided comparable results.