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We report for the first time the occurrence of at least two species of the phylum Gnathostomulida in the Southern Ocean, along the shores of the Ross Sea in Antarctica. At least one species for each of the orders of the phylum (Filospermoidea and Bursovaginoidea) was found using both morphological inspection and DNA metabarcoding of the shallow marine sediments collected with a Van Veen grab or by scuba diving in the area facing the Italian research station “Mario Zucchelli”.