In numerous taxa, studies have reported the co-occurrence of several copies for a single mitochondrial marker (heteroplasmy), leading to incorrect phylogenetic inferences if not detected. While this phenomenon has been widely investigated in terrestrial taxa, it remains largely unexplored in marine algae. Here we report the detection of heteroplasmy in the Lessonia nigrescens species complex. This work aimed to identify the distinct fragments and to determine their geographic extent in the distribution range of two kelp species. Using phylogenetic reconstructions of a mitochondrial DNA marker (atp8/trnS intergenic region), we suggest that a duplication event occurred, either with or without transfer of the copy to the nucleus. The corresponding sequences constituted a new monophyletic clade, distinct from those previously described in L. nigrescens, hence discarding the interspecific hybridization and intraspecific biparental transmission hypotheses. The characterization of 652 individuals sampled along 2,500 km of coastline revealed that the duplication was absent in the Northern species, but of high frequency in the northernmost populations of the Southern species. Because the duplication is restricted to the parapatric contact zone between the two species, our findings open new perspectives about the importance of reproductive isolation mechanisms and local adaptation in the origin and persistence of this pattern.