The hard clam, Mercenaria mercenaria , is extensively cultured along the Atlantic seaboard of the U.S. Maintenance and growth of this aquaculture industry relies on hatchery production of seed, and billions of seed clams are produced annually to fulfill aquaculture and restoration needs. Several states regularly suffer losses in hard clam stocks due to disease (e.g. QPX in the Northeast) and environmental stress (e.g. heat waves in Florida). Therefore , the production of quality seed able to survive under harsh biological and environmental conditions represents a priority for the aquaculture community. This collaborative initiative builds on ongoing cooperation and new partnerships among Sea Grant programs, scientists and extension teams in five Atlantic states to develop a hard clam selective breeding program using state of the art genomic tools, for the benefit of clam farmers throughout the region. The team has just completed the sequencing and assembly of the hard clam genome and is currently re-sequencing clams collected from Maine to Florida to gather information about the genetic diversity of the species throughout its natural range in the U.S. Generated genomic data will be used to develop an efficient and cost-effective genotyping platform (SNP array) for M. mercenaria. This genotyping platform will enable genome-assisted selection for traits relevant to various regions supporting the growth of the hard clam aquaculture industry. These activities will serve as a basis to establish clam breeding programs linking scientists, extension networks and the industry to provide growers with superior clam stocks.