Sargassum natans and Sargassum fluitans are uniquely holopelagic macroalgae, providing open ocean nursery and foraging habitat for commercially and ecologically important species. Recent basin‐wide changes in pelagic Sargassum diversity and distribution have manifested in proliferation of a previously rare morphotype, Sargassum natans VIII, to rival biomass levels of historically dominant S. natans I and S. fluitans III. Precise genetic identification of these morphotypes can improve accuracy and interpretation of ecological studies as well as clarify evolutionary history and population connectivity. For 139 field samples collected from the subtropical and tropical North Atlantic, three mitochondrial genes (cox3, nad6, and mt16S rRNA) were used to examine genetic divergence among the three common pelagic Sargassum morphotypes. These gene sequences successfully differentiated among morphotypes regardless of geographic origin, confirming in situ morphology‐based identifications. Sargassum natans I and S. natans VIII exhibited divergence consistent with that between the S. natans‐complex and S. fluitans III. Phylogenetic analysis of these samples also indicated evolutionary divergence between Sargassum morphologies. The genetic divergence among morphotypes, compared with benthic Sargassum species, suggested that taxonomic reclassification of the three most common pelagic morphotypes may be warranted.
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