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In this study, a microsatellite-based multiplex PCR panel for meagre (<i>Argyrosomus regius</i>) was developed as a useful and single tool in parental assignment and population studies. Twenty-one specific and interspecific microsatellites from different aquaculture species of meagre (<i>Argyrosomus regius</i>), Japanese meagre (<i>A. japonicus</i>), red drum (<i>Sciaenops ocellatus</i>) and yellow meagre (<i>Acoupa weakfish</i>) were assessed for genetic variability, allelic range and genotype reliability. Finally, a SuperMultiplex for <i>Argyrosomus regius</i> (SMAr) was designed with only the best eight microsatellite markers. The panel assessment was performed using a batch of brood stock from one company and a sample of 616 offspring. It was possible to assign 95% of the offspring to a single pair of parents using the exclusion method. It is therefore considered an easy procedure, and a powerful and low-cost tool for parental assignment to support companies’ breeding programs and to exchange information between research groups.