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Abstract: A large majority of Atlantic cod (Gadus morhua) found all year round in outer parts of fjords and along outer coastal areas in general in northern Norway have a genetic signature at the pantophysin (Pan I) locus that distinguish them from Norwegian coastal cod (NCC) found further inside fjords in the same areas. The identity of these fish has been controversial and to examine if they represent a distinct coastal cod group, or are identical to the migratory North East Arctic cod (NEAC) of the Barents Sea, a comparison was conducted at 10 microsatellite loci for 15 samples comprising each of the three groups inner coastal NCC, outer coastal cod and NEAC. Spatial analysis of molecular variance revealed that the outer coastal samples cannot be discriminated from NEAC by means of microsatellite markers, supporting the similarity of the two groups at the Pan I locus. This implies that a portion of the otherwise migratory NEAC, at least in its premature stage, remains in coastal areas in close contact with the genetically quite distinct NCC group. Both the coalescent-based simulation approach and the lnRH test for selective sweeps proved two of the microsatellite loci, GMO 34 and GMO 132 to be non-neutral. Notwithstanding, these two loci, together with the acknowledged non-neutral Pan I locus, which displayed profound linkage disequilibrium to GMO 34 within NEAC, are as yet the only nuclear markers which unambiguously discriminate between NEAC and NCC. Although the relative contribution of restricted gene flow versus selection as a causative agent for the divergence between NEAC and NCC has not been assessed, we believe the magnitude of differentiation at the three loci provides rational for maintaining NEAC and NCC as separate management units. [Copyright &y& Elsevier]