Global molluscan aquaculture production is continuously increasing, dominated by five species, among which the Pacific cupped oyster, Crassostrea gigas, predominates. Hatchery production is accompanying this increase to assist consistent availability of juveniles for restocking, fishery enhancement, genetic improvements as well as for species diversification. Hatchery development contributes significantly to the demand for international transfers of live molluscs; a consequence of which pathogen transfer via transfer of live molluscs is currently recognised as a major cause of epizootic disease outbreaks. Diseases are a primary constraint to mollusc aquaculture growth and sustainability, severely impacting socioeconomic development in many countries. Several diseases which occur in hatcheries could be disseminated with live transfers to grow-out areas. On the other hand, hatchery production may also be a way to provide disease-free juveniles and therefore be a pivotal tool to prevent the transfer of infected stocks to susceptible areas. After reviewing the importance of hatcheries for molluscs and mollusc diseases in hatcheries, this paradox in health risk and management is discussed.