Northern quahogs Mercenaria mercenaria are bivalve mollusks found in the intertidal to subtidal zones of shallow, protected coastal embayments from the southern Gulf of St. Lawrence to the Gulf of Mexico. Canadian populations deserve recognition as stocks distinct from the larger population of the U.S. Atlantic coast. Although the hard clam occupies a virtually continuous range from Florida to Massachusetts, its distribution north of Cape Cod becomes disjunct. Two populations have been documented in the Bay of Fundy region of Atlantic Canada, one of which in St. Mary’s Bay, Nova Scotia, Canada. However, details on their origin and actual population structure have never been described (LeBlanc et al. 2005).