The southern Italian peninsula has been suggested to be an important European district for lampreys’ genetic diversity. All lamprey species ever described throughout the Italian peninsula are protected within European legislation and listed in Annex II of the EU Habitats Directive (92/43/EEC) and Annex III of the Bern Convention (82/72/CEE) as species of conservation concern, and the Habitats Directive ensures the designation of “sites of community interest” (SICs) for threatened species. During a survey to collect preliminary data on lampreys’ presence in the Cilento, Vallo di Daino, and Alburni National Park (PNCV) located in the Campania region, where 28 sites of community interest (SICs) have been established by the EU Habitats Directive (92/43/EEC), two specimens of sea lamprey (Petromyzon marinus, Linnaeus, 1758) were detected for the first time. The specimens were genetically characterized through the sequencing of the mtDNA control region locus. The study highlighted the significant importance of the Campania region for lampreys, which, concerning Lampetra sp., was found to have peculiar genetic characteristics and unique alleles that have not been described elsewhere. Furthermore, the recognition of the sea lamprey, P. marinus, emphasized the value of this area, especially in terms of laying the groundwork for future habitat protection strategies.