Atlantic mackerel (Scomber scombrus) ranks among the most valuable fish species in Europe. The NE Atlantic mackerel population is considered to comprise three main stocks (southern, western and North Sea), with variable proportions of these three intermixing at the northerly feeding grounds. The southern and western mackerel stocks have moved over the past 4–5 years further north- and westward. Consequently, large-scale mackerel fishing and processing have become thriving industries in Iceland and the Faroe Islands in just a few years. The mackerel population structure in the Mediterranean Sea is less well known but seems to comprise at least one, more or less isolated, spawning component. Although mackerel is an important food resource, systematic and concerted epidemiological surveys of Anisakis species in Atlantic mackerel from European fishing grounds have been lacking. As part of the EU FP7 PARASITE project (GA no. 312068), occurrence and specific identity of Anisakis spp. from 1801 mackerel from Northeast Atlantic and Mediterranean waters was investigated. In general, mackerel caught at the Atlantic fishing grounds exhibited markedly higher Anisakis spp. infection levels than fish from the Mediterranean localities. Mackerel caught off NW Spain and Portugal (ICES VIIIc, IXa) showed highest overall and muscular prevalence, reaching 87% and 52%, respectively, which differed significantly from all other Atlantic samples. Lowest overall Anisakis spp. prevalence and abundance was recorded in mackerel from Faroe Isles waters, while lowest muscular infection levels were found in the samples from the North Sea. Genetic nematode species identification showed that A. simplex (sensu stricto) is the dominating species in mackerel from the Atlantic areas, while A. pegreffii dominated in the samples from the Mediterranean Sea. The latter species showed generally low prevalence and intensity in the flesh, not exceeding 6% and one larva, respectively. While A. simplex (s. s.) and A. pegreffii seem to co-occur in mackerel from off NW Spain and Portugal, several A. pegreffii were also recorded in mackerel from the North- and Norwegian Seas. These findings imply that the actual mackerel started their feeding migration in waters south to the British Isles, which include parts of the sympatric area of the two sibling species. Thus, A. pegreffii could prove a useful supplementary marker to track migration routes of the different mackerel stock components in NE Atlantic waters.