The application of molecular systematics to the anisakid nematodes of the genera Anisakis, Pseudoterranova and Contracaecum, parasites of aquatic organisms, over the last two decades, has advanced the understanding of their systematics, taxonomy, ecology and phylogeny substantially. Here the results of this effort on this group of species from the early genetic works to the current status of their revised taxonomy, ecology and evolutionary aspects are reviewed for each of three parasitic groups. It has been shown that many anisakid morphospecies of Anisakis, Contracaecum and Pseudoterranova include a certain number of sibling species. Molecular genetic markers provided a rapid, precise means to screen and identify several species that serve as definitive and intermediate and or/paratenic hosts of the so far genetically characterized species. Patterns of differential distribution of anisakid nematodes in various definitive and intermediate hosts are presented. Differences in the life history of related species can be due both to differential host-parasite co-adaptation and co-evolution, and/or to interspecific competition, that can reduce the range of potential hosts in sympatric conditions. Phylogenetic hypotheses attempted for anisakid nematodes and the possible evolutionary scenarios that have been proposed inferred from molecular data, also with respect to the phylogeny of their hosts are presented for the parasite-host associations Anisakis-cetaceans and Contracaecum-pinnipeds, showing that codivergence and host-switching events could have accompanied the evolution of these groups of parasites. Finally, examples in which anisakid nematodes recognized genetically at the species level in definitive and intermediate/paratenic hosts from various geographical areas of the Boreal and Austral regions and their infection levels have been used as biological indicators of fish stocks and food-web integrity in areas at high versus low levels of habitat disturbance (pollution, overfishing, by-catch) are presented.