In the present paper, recent results obtained on the use of different distributions observed in larval species of Anisakis, genetically identified by means of allozyme markers, for stock characterization of demersal (Merluccius merluccius), small (Trachurus trachurus) and large pelagic (Xiphias gladius) finfish species in European waters, are reviewed and discussed. Several species of Anisakis were identified in the three fish hosts: A. simplex (s.s.), A. physeteris, A. typica, A. ziphidarum,A. pegreffii, A. brevispiculata and A. paggiae. Canonical discriminant analysis performed on all the samples of the three fish species collected in areas comprising their geographical range, according to the different species of Anisakis identified, showed distinct fish populations in European waters. In all the three fish hosts, the pattern of distribution of Anisakis larvae allowed discrimination of Mediterranean stocks from Atlantic stocks. In the case of swordfish, the possible existence of a southern Atlantic stock separated from a northern one is also suggested. Congruence and discordance with the population genetic data inferred from allozyme markers on the same samples of the three fish species are also discussed.