Analysis of geographic variation in the frequencies of alleles at the Tf locus in Atlantic cod, G. morhua, indicates that it is possible to distinguish 3 major populations off eastern North America: north of the Laurentian Channel; south of the Laurentian Channel and Flemish Cap. The data also suggest that the north Laurentian stock may be further subdivided into a northern and southern component. The genetic distinction between the cod population on Flemish Cap and those on other areas of the continental shelf is confirmed by a significant difference in allele frequencies at the PG1-2 locus. It is suggested that the cod population on Flemish Cap may have persisted in isolation since the last glaciation.