Facing an alarming continuing decline of wild sea cucumber resources, management strategies were developed over the past three decades to sustainably promote development, maintenance, or regeneration of wild sea cucumber fisheries. In New Caledonia (South Pacific), dedicated management efforts via restocking and sea ranching programs were implemented to cope with the overharvesting of the sandfish Holothuria scabra and the recent loss of known populations. In order to investigate genetic implications of a major H. scabra restocking program, we assessed the genetic diversity and structure of wild stocks and hatchery-produced sandfish and compared the genetic outcomes of consecutive spawning and juvenile production events. For this, 1,358 sandfish collected at four sites along the northwestern coasts of New Caledonia, as well as during five different restocking events in the Tiabet Bay, were genotyped using nine polymorphic microsatellite markers. We found that wild H. scabra populations from the northwestern coast of New Caledonia likely belonged to one panmictic population with high level of gene flow observed along the study scale. Further, this panmictic population displayed an effective size of breeders large enough to ensure the feasibility of appropriate breeding programs for restocking. In contrast, hatchery-produced samples did suffer from an important reduction in the effective population size: the effective population sizes were so small that genetic drift was detectable over one generation, with the presence of inbred individuals, as well as more related dyads than in wild populations. All these results suggest that dedicated efforts in hatcheries are further needed to maintain genetic diversity of hatchery-produced individuals in order to unbalance any negative impact during this artificial selection.