Macrocystis pyrifera is ecologically and commercially important seaweed; therefore, it is a well-studied species in terms of its morphology, geographical distribution and its economic uses in Peru. However, research on its genetic structure is scarce. A recent study conducted along the Southeastern coast of the Pacific, concluded that Macrocystis has low genetic variability. Nevertheless, this research unraveled a different genetic pattern in Peru, including unique haplotypes in two sites. The aim of this study was to analyze the genetic variability of M. pyrifera, using the mitochondrial markers atp8-S, in eight locations covering 2500 Km of coastline from Peru. With 57 sequences analyzed, the results showed low haplotype (He= 0.562) and nucleotide (π= 0.00480) diversity. Paired analysis distributions and the number of paired differences (k) were equal to 0.619. Four haplotypes were found: (1) The putative ancestral haplotype (Mpyr1), widely distributed in the study area, also reported in central Chile, (2) A shared haplotype between populations from southern Peru and northern Chile (Mpyr2) and (3) Two new haplotypes: (Mpyr8) from San Lorenzo Island, and (Mpyr9) from Los Bancos and San Nicolas Bay, Peru.