The present study investigates the planktonic communities through metagenomics sequencing during a mucilage event in the Çanakkale Strait (Dardanelles), Turkey. Mucilage samples were collected in May 2021 during an intense period of mucilage formation in three different stations of Dardanelles (Station 1: 40°9'8.09"N, 26°24'16.19"E; Station 2: 40°6'21.62"N, 26°22'41.25"E; Station 3: 40°6'42.78"N, 26°23'57.00"E). The dominant planktonic eukaryotes, at the phylum level, were Dinoflagellata (38.57%), Protalveolata (15.03%), Diatomea (12.41%), Nematozoa (8.44%), Apicomplexa (6.79%) and Chlorophyta (5.43%), which constituted 86.68 % of the total number of sequences. The most dominant OTUs (>10%), were Alexandrium and Syndiniales Group II. other dominant OTUs (>2%) were Viscosia sp., Lankesteria, Arcocellulus, Thalassiosira and Nannochloris. This study has clarified the situation of planktonic communities during a mucilage event in the Çanakkale Strait (Dardanelles), Turkey. As a result, the most dominant genus was Alexandrium, which has been known to produce mucilage. Some Alexandrium species can produce toxins, cause severe impacts on human health, and lead to bivalve, shrimp, and fish mortality. Therefore, a more detailed study is needed to determine the Alexandrium toxins in the mucilage structure. In addition, the heavy metal content of the obtained mucilage was investigated, and the concentrations of the As and Cr are above the disposal limits in the landfill sites. Therefore, collected mucilage from the sea surface should be checked before sending it to landfill sites in terms of the heavy metal content.