Many macroalgae exhibit considerable intraspecific morphological variation, but whether such variation reflects phenotypic plasticity or underlying genetic differences is often poorly understood. We quantified both morphological and genetic variation of 96 plants from seven field sites across eastern South Island, New Zealand, to assess genetic differences between morphotypes of the southern bull kelp Durvillaea antarctica (Cham.) Har. Consistent DNA sequence differentiation across mitochondrial, plastid, and nuclear loci was correlated with two broadly sympatric morphotypes: “cape” and “thonged.” These ecologically, morphologically, and genetically distinct bull-kelp lineages were previously considered to be environmentally determined phenotypes with no underlying genetic basis. Interestingly, the sheltered “cape” lineage appears essentially genetically uniform across its South Island range, whereas the exposed “thonged” lineage exhibits marked phylogeographic structure across its range. Results suggest that D. antarctica in New Zealand comprises two reproductively isolated species.