In this study, we researched the presence of anisakids in specimens of Merluccius merluccius caught in the area of Little Sole Bank, in the Northeast Atlantic, and found that 100% of the European hake examined were infected and showed high average values of abundance (976.88) and intensity (976.88). The larvae were identified in morphological terms as morphotype type I and in molecular terms as Anisakis simplex s.s via polymerase chain reaction (PCR) restriction fragment length polymorphism of the rDNA. The genetic variability of the A. simplex s.s population in the North Atlantic is notable, with at least two ribosomal and three mitochondrial haplotypes which are different from the specimen used as control, reflecting the diversity of this species, an aspect which has scarcely been studied to date. The cox-2 gene appears to be an interesting candidate for generating new genetic markers which can be applied to differentiate between A. simplex s.s and Anisakis pegreffii. We detected 11 fixed differences in this gene, and it also offers the advantage of being easily amplified by PCR. The high prevalence of infection by A. simplex s.s and the extremely high average intensity and abundance values can have significant repercussions on public health, especially among populations which regularly eat insufficiently cooked or raw fish and have a certain genetic predisposition; the genetic variability of the parasite could be another factor to take into account.