During the past decade, genetic markers have been used increasingly to improve stock discrimination and to aid fisheries management. Today, the Icelandic and Faroese Plateau cod (Gadus morhua) are managed as separate units, belonging to ICES Subareas Va and Vb1, respectively. There is little information on the genetic connectivity of the two units, however, except in terms of tagging experiments which revealed limited adult migration between the two areas, and few genetic studies describing genetic differentiation among Faroese and East Icelandic cod. Here, previously published data on the genetic structure of Icelandic cod were combined with new data from the Faroe Plateau to assess the level and the source of genetic variability of Atlantic cod around the Iceland–Faroe Ridge and the potential sources of genetic variation. In all, 771 cod were genotyped at nine microsatellite loci and at the Pantophysin locus (Pan I). The genetic markers employed were congruent and showed that South Icelandic and East Icelandic–Faroese Plateau populations have limited genetic connectivity. Diversifying selection associated with restricted gene flow is likely to explain the observed pattern with the Pan I locus. Further analyses detected historical imprints in the microsatellite data, suggesting that the divergence could be due to isolation of different cod populations during the last glacial maximum.