The blackspot seabream, Pagellus bogaraveo, is a sparid fish of great economic importance in the northeast Atlantic. The main aim of this work was to assess the infection levels and diversity of anisakid nematodes parasitizing P. bogaraveo from Portuguese waters. The anisakid larvae were identified by polymerase chain reaction-restriction fragment length polymorphism analysis and ten different patterns were observed, four of which were not previously reported in the literature. Moreover, several species were detected for the first time in this host: Anisakis simplex × Anisakis pegreffii hybrids, Anisakis ziphidarum, Anisakis typica, Anisakis physeteris, as well as three undescribed anisakids Anisakis sp. PB-2009, Anisakis sp. PB-2010, and Contracaecum sp. PB-2010. The ITS1-5.8S-ITS2 region was sequenced and analyzed phylogenetically, revealing that our anisakids were distributed by the two distinct clades reported previously, corresponding to the two recognized larval morphotypes. Moreover, a group of organisms, including our specimens from Madeira and the previously reported Anisakis sp. HC-2005, cluster together and seem to belong to clade I. A certain degree of intraspecific diversity was also detected. Samples from mainland waters had the highest infection levels and were dominated by A. pegreffii. Madeira had the highest diversity overall, dominated by Anisakis sp. PB-2010. Fish from the Azores had the lowest infection levels, and the species with the highest relative abundance was A. physeteris. The anisakid nematode communities were relatively similar in mainland waters but very distinct in both the Azores and Madeira islands, suggesting the existence of at least three different stocks of P. bogaraveo in the northeast Atlantic.