The bay scallop (Argopecten irradians) is a species of substantial economic and ecological importance, found along the U.S. Atlantic coasts, from New England to the Gulf of Mexico (Fig. 1). Despite its significance, populations of A. irradians have suffered significant declines due to factors such as overfishing, habitat degradation, climate change, and disease outbreaks. In 2019, New York’s bay scallop population was devastated by a mass mortality event linked to an outbreak of the apicomplexan parasite Bay Scallop Marosporida (BSM). This event, driven by rising water temperatures, highlighted the urgent need for genomic data to better understand and protect A. irradians populations. Genomic data can be crucial for developing strategies such as marker-assisted and genomic selection, which could improve scallop resilience to environmental stressors and disease. Historically, A. irradians has been divided into three extant subspecies: A. irradians irradians, found along the Atlantic coast from Massachusetts to North Carolina; A. irradians concentricus, distributed along the Gulf of Mexico; and A. irradians amplicostatus, primarily located in the western Gulf. Although these subspecies exhibit subtle phenotypic differences, they are difficult to distinguish based solely on physical traits. Our genomic analysis aimed to fill the gap in knowledge regarding these subspecies, as most previous genomic data were limited to scallops introduced to China from the USA and Canada in the 1980s and 1990s. This study harnesses advanced genomic techniques, including genotyping-by-sequencing (GBS) and whole-genome sequencing (WGS), to investigate the genetic and genomic diversity of the species, with the goal of informing future conservation strategies and improving aquaculture practices. The study involved sequencing and analyzing 960 scallop samples from six U.S. states. Our findings revealed significant genetic differences across populations, with distinct clustering based on geographic regions. By identifying genetically distinct populations and understanding their evolutionary history, this research establishes a basis for targeted management practices to help protect bay scallop populations from disease threats and global environmental changes.