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A recent molecular investigation of kelp systematics revealed mitochondrial sequences that gave phylogenies inconsistent with those based on nuclear and chloroplast sequences for the species Lessoniopsis littoralis. Sequence from the mitochondrial nad6 region placed L. littoralis in the middle of a clade of Alaria species in our trees, whereas Rubisco and nuclear ribosomal DNA sequences resolved L. littoralis within the Alariaceae, but distinct from Alaria. To resolve these conflicting results, the nad6 region was sequenced from additional samples of L. littoralis. The resulting data variously placed L. littoralis with Macrocystis integrifolia, Nereocystis luetkeana, and an additional Alaria isolate. A series of hypotheses were devised and explored to effectively exclude introgression via hybridization as a viable explanation for our observations. Rather, molecular and microscopy data revealed that gametophytes of Alaria, Macrocystis and Nereocystis epi/endophytically, colonize the older portions of the thallus of L. littoralis. A substantial primer mismatch, unique to L. littoralis, was uncovered subsequently explaining why nad6 sequences from only Alaria, Macrocystis and Nereocystis were amplified from L. littoralis sporophyte samples, although the DNA from the gametophytes likely represented only a small percentage of the total DNA extracted.