Hatcheries are critical for seed production of commercial aquaculture species, and vital in supporting wild population recovery and augmentation efforts, selective breeding programmes and conservation management. For many broadcast and mass-spawning species however, they can be capricious environments where genetic diversity may be lost due to small effective broodstock population sizes, variable broodstock contributions and differential survival of family groups, thus impacting the genetic fitness of offspring cohorts. Assessment of genetic variability in cultured species is therefore critical for addressing these problems and optimising propagation methods. This study used 6,051 genome-wide SNPs to analyse the genetic diversity, parental contributions and kinship of offspring during a commercial-scale hatchery production run of sandfish (Holothuria scabra ), a high-value sea cucumber grown in mariculture operations across the Indo-Pacific region. Broodstock contributions were found to be highly skewed, with up to 26% of the total parent pool contributing and kinship analyses determined that just two parents sired between 44.4-67.5% of all offspring genotyped. Effective population sizes were reduced as expected between broodstock and offspring groups (NeLD =1,121.2 vs. 19.4, respectively), while losses of allelic diversity but not overall heterozygosity were apparent. Numbers of families surviving (13-16) to the juvenile stage were low, suggesting low effective population sizes among offspring cohorts is an issue for sandfish hatchery operations. To address variability in family compositions and broodstock contributions, pedigree tracking and batch spawning may be used to optimize broodstock management and hatchery protocols, to ensure production of genetically diverse offspring for routine culture and restocking operations. Given that many sandfish broodstock are sourced from the wild, the maintenance of healthy wild populations is crucial as reservoirs of genetic diversity. Furthermore, selecting distantly-related genetically diverse individuals for spawning, is recommended to enhance the genetic fitness of sandfish populations within hatchery settings.