Allozymes and restriction fragment length polymorphisms (RFLP's) in genes of the NADH dehydrogenase complex (ND 5/6 genes) of mitochondrial DNA (mtDNA) were used to investigate the spatial genetic structure of Atlanto-Scandian herring (Clupea harengus). Samples (sample size=46–50/site) comprised Icelandic summer spawners, Norwegian spring spawners, and two fjord populations, Balsfjord and Trondheimsfjord, on the Norwegian coast. Fifty enzymes were assayed, and samples were routinely examined at 18 enzymes comprising 28 putative allozyme loci. Significant genetic differentiation (P < 0.001) was detected between Trondheimsfjord herring and all other samples, with apparent genetic homogeneity among remaining samples, including the Balsfjord; a region shown previously to contain an allozymically distinct population. Herring from the Balsfjord were shown allozymically to represent the Norwegian spring spawning group, suggesting the presence of two stocks, a deeper resident spawning (Balsfjord) and a shallower, non-native feeding population (Norwegian spring spawning). Variation at the ND5/6 genes using six restriction enzymes revealed 96 composite haplotypes in 196 fish. Mean haplotype diversity was high (0.92), though nucleotide divergence between samples was small (highest=0.00029, between Trondheimsfjord and Balsfjord samples; lowest=0.00003, between Icelandic summer and Balsfjord samples). Monte-Carlo %2 analysis of haplotype frequencies revealed no significant geographic heterogeneity among samples, thus revealing a discordant pattern of genetic differentiation produced by allozymes and mtDNA markers. The detection of a genetically divergent population in deeper waters of the Trondheimsfjord supports the existence of distinct deep-water resident populations in the Norwegian fjords.