The kelp genus Eisenia Areschoug is represented by two species in the Southeast Pacific: Eisenia cokeri, distributed in Peru and Chile, and E. gracilis, endemic to Peru. However, the taxonomic distinction between these two species has been questioned. Additionally, it is uncertain whether E. cokeri is conspecific with the Northeast Pacific species E. arborea. To address these issues, we examine, for the first time, the morphology and the molecular phylogenetics of E. cokeri and E. gracilis across their geographic range. Sampling for morphological and molecular analyses was conducted at subtidal zones in five locations in Peru. Furthermore, a locality in Chile was sampled for molecular studies, where E. cokeri was documented. Peruvian Eisenia species exhibited notable differences in morphological characters, including size, holdfast diameter, stipe modifications (e.g., longitudinal division and pseudostipe formation), frond division, frond margins, and roughness, as evidenced by differences in thallus morphometric variables. Phylogenetic analyses using mitochondrial and chloroplast markers revealed three distinct genetic lineages and two endemic species: E. cokeri and E. gracilis from Peru, and a new Eisenia sp. from Chile. Moreover, we confirmed the distinctiveness of E. cokeri from E. arborea and provided updated information on the distribution of E. cokeri and E. gracilis in the Southeast Pacific. These findings are crucial for the management and conservation of these endemic, foundational species.