The pustulose ark, Anadara tuberculosa, is considered as an emblematic species of the east Pacific mangrove ecosystem. The decline of its populations is of increasing preoccupation, in particular in Peru. The use of hatchery-produced larvae for stock enhancement or aquaculture is attractive but raises strong criticisms from an ecological point of view, as it could conduce to loss of genetic diversity in wild populations and favor the disease spreading from hatcheries to the environment. In this works, spat production through traditional aquaculture/biotechnology technologies was associated with pathogen molecular diagnostics and with genetic diversity estimation to produce specific pathogen-free (SPF) larvae from genetically characterized populations. All PCR and nested-PCR diagnostics of common bivalve pathogens, such as Bonamia, Martelia, Perkinsus and OsHV1, led to negative results for healthy or moribund adults and spat samples. Microbiological and molecular analyses realized during mortalities led to identifying a pathogenic Pseudomonas strain present on culture tank walls, in moribund spats and adults´ blood. Population genetic variation was assessed by mitochondrial COI gene sequences which showed 36.7% haplotype diversity. This study with hatchery production, pathology and genetic components for an overexploited native bivalve represents an original model for successful mollusk stock enhancement or/and innovative aquaculture programs.