Parental contributions of giant grouper to communal spawns in captivity is important for establishing genetic management of the species. In this study, we have followed the spawning dynamics of three males and three females over six to eight consecutive days, over three time periods. Polymorphic microsatellite markers were validated and utilised to successfully determine parentage in 574 offspring from 20 nights of spawns. Variation of both maternal and paternal contributions between nights in batches of spawns were significant (P < 0.001). Most paternal assignments were attributed to one dominant male who initiated each spawning batch, however, all males and females successfully mated over the spawning period. There was a significant (P < 0.01) trend towards a polygamous reproductive mode for giant grouper: in two of the three batches of spawns, where on some nights, eggs from all females were fertilised by multiple males. Genetic variation was assessed between parents and offspring. There was a loss of alleles on each spawning night, however, if offspring from a series of consecutive nights were combined, most or all of the genetic variation would be maintained in the F1 generation. This research validates the use of molecular tools for genetic monitoring of giant grouper and improves the understanding of spawning dynamics of protogynous hermaphroditic communal spawners over time in an aquaculture setting.