Abstract. Sriwijayanti LA, Djumanto, Setiawan RY, Firdaus MR, Fitriya N, Sugeha HY. 2019. Community structure of phytoplankton in the surface and thermocline layers of Sangihe and Talaud waters, Indonesia. Bonorowo Wetlands 9: 51-58. The aim of this study was to determine the species dominance and distribution, and community structure of phytoplankton in the surface and thermocline layers of Sangihe and Talaud waters Indonesia. Phytoplankton samples were collected at the Sangihe-Talaud waters in October 2018 at 14 research stations. Water samples were collected at 5 m (surface) and thermoclines layers using rosette sampler equipped with Conductivity, Temperature, and Depth (CTD) recorder. Samples were concentrated to 40 ml using hand plankton net (mesh size 20 µm), then preserved with 4% formaldehyde. Phytoplankton species were identified using a guidebook based on morphological character traits. The cell count of each species of plankton was calculated using a Sedgwick rafter counting cell chamber. The result showed that there were 4 classes of phytoplankton (Bacillariophyceae, Dinophyceae, Cyanophyceae, and Raphydophyceae) which consisted of 59 species in the surface and 56 species in the thermocline, respectively. The abundance of phytoplankton at surface ranged from 77,333-4,024,000 cell m-3, meanwhile in the thermocline layer 8,000-542,222 cell m-3. The average of phytoplankton diversity of the surface was 0.82 and the thermocline was 1.71. The surface layer was dominated by Leptocylindrus danicus (8.92 x 106 cell m-3), Trichodesmium erythareum (5.83 x 106 cell m-3), and Detonula converfacea (0.62 x 106 cell m-3). The thermocline layer was dominated by Chaetoceros affinis (2.74 x 105 cell m-3), Thalassionema nitzchioides (2.21 x 105 cell m-3), and Chaertoceros dichaeta (1.38 x 105 cell m-3). The low phytoplankton abundance was found at the stations 12 and 13 caused by higher salinity concentration. The highest phytoplankton abundance was found in the stations with warmer temperatures, both in the surface and in the thermocline. The shallow depth thermocline layer (75-100 m) has a higher abundance than the deeper thermocline layer (110-150 m). Temperature was the environmental parameter that has the greatest influence on the abundance and species of phytoplankton, the phytoplankton in the surface layer reached 10 times more abundant than the thermocline layer.