The longfin squid Loligo pealeii is distributed widely in the NW Atlantic and is the target of a major fishery. A previous electrophoretic study of L. pealeii was unable to prove genetic differentiation, and the fishery has been managed as a single unit stock. We tested for population structure using 5 microsatellite loci. In early summer (June), when the squids had migrated inshore to spawn, we distinguished 4 genetically distinct stocks between Delaware and Cape Cod (ca. 490 km); a 5th genetic stock occurred in Nova Scotia and a 6th in the northern Gulf of Mexico. One of the summer inshore stocks did not show genetic differentiation from 2 of the winter offshore populations. We suggest that squids from summer locations overwinter in offshore canyons and that winter offshore fishing may affect multiple stocks of the inshore fishery. In spring, squids may segregate by genetic stock as they undertake their inshore migration, indicating an underlying mechanism of subpopulation recognition.