We present evidence of mitochondrial and nuclear introgression from the Atlantic herring Clupea harengus into the Pacific herring C. pallasii in northern European seas, where the two species have come into secondary contact following the post-glacial trans-Arctic invasion of Pacific herring to the Atlantic realm. Although the breeding areas of the two species are thought to be separate, 7 % of the resident Pacific herring in samples from the White Sea were found to possess Atlantic herring mitochondria. The percentage was even higher (21 %) in the local Balsfjord stock of the Norwegian Sea, whereas it was nil in Pechora Sea samples. Similar or somewhat lower levels of genomic admixture were estimated from four diagnostic or nearly diagnostic nuclear allozyme loci. The absences of inter-locus and cytonuclear disequilibria, together with the patterns of mtDNA haplotype diversity, suggest recurrent backcrossing and hybridization over a long period in the post-glacial time frame. From a reassessment of published