The hard clam, Mercenaria mercenaria, is extensively aquacultured from Massachusetts to Florida. The maintenance and growth of this aquaculture industry rely on hatchery production of seed clams, with billions produced annually to fulfill aquaculture and restoration needs. In this context, the production of quality seed capable of surviving under harsh biological and environmental conditions is a major priority for the aquaculture community. This collaborative project builds on partnerships between Sea Grant programs, scientists and extension teams in five Atlantic states to develop hard clam selective breeding programs using state of the art genomic tools. In this framework, the team produced a chromosome-level assembly of the clam genome and used that resource as a reference for the characterization of the species genetic diversity across its range. Through a series of stringent selection criteria, single nucleotide polymorphisms (SNPs) identified in M. mercenaria were filtered and a subset of 66,543 SNPs was used to produce SNP arrays for high-throughput genotyping of clams (Figure 1). The array incorporates markers for detecting the clam pathogen Mucochytrium quahogii (formerly Quahog Parasite Unknown, a.k.a. QPX), enhancing its utility in disease management. Performance evaluation highlighted the importance of sample preservation on genotyping results, while concordance testing demonstrated the array’s reliability, with an average allele call agreement of 99.64% across multiple tissue types. More importantly, the produced arrays showed high efficiency and robustness in differentiating clams from different geographic origins and in contrasting the genotypes of clams resistant or susceptible to QPX disease and heat stress. Overall, the produced array represents a powerful and robust genotyping tool offerring unprecedented insights into the species’ genomic architecture and population dynamics. Genomic selection using this tool is ongoing to identify clam stocks resistant to QPX disease and heat stress. Through coordination and extension, we are working to transform hard clam aquaculture by promoting the use of these modern approaches to enhance industry sustainability and resilience.