An ecologically particularly important group of eukaryotic microorganisms in Antarctic shallow water coastal zones are benthic diatoms living on top of, or associated with sediments or rocks. Their benthic assemblage exerts multiple important functions as high primary producers, providing a major food source for a diversity of organisms such as bacteria by excretion of soluble organic matter, benthic protozoans as well as metazoans. Despite their crucial role, information about the biodiversity of Antarctic marine benthic diatoms is scarce and only a few studies exploring their biodiversity exist. DNA metabarcoding (rbcL and 18SV4 genes) were used to access the concealed biodiversity of benthic diatoms in Potter Cove (King George Island, Antarctic Peninsula) beyond the limits of morphological and cultivating methods to assess the status of the taxonomic coverage in this region.