Abstract: Phytoplankton net samples were collected in the south sector of Eastern Indian Ocean (10.0°S-4.0°N, 83.0°E-97.5°E) from March 13 to May 7, 2013.Phytoplankton community structure features were analyzed, including species composition, ecotypes, cell abundance, dominant species, and diversity.To understand the inter-annual variation of phytoplankton community under the context of climate change, we also compiled previous phytoplankton community data in the 1960s and 2013, and compared with present study.Of the 350 taxa (including variation, form and unidentified taxa), 162 taxa of 48 genera in Bacillariophyta, 183 taxa of 24 genera in Dinophyta and 4 taxa of 2 genera in Chrysophyta were recorded.The dominant phytoplankton ecotypes were tropical oceanic species and warm oceanic species.The dominant species were mostly Bacillariophyta, such as Planktoniella formoa, Nitschia spp.Chaetoceros spp., Climacodium frauenfeldianum and Pseudosolenia calcaravis, while the others belonged to Dinophyta (Pyrocystis noctiluca and Neoceratium trichoceors).The highest cell abundance of 140.3×10³ cells/m³ were recorded in the southeast of surveyed area, and intermediate level of 10⁴ cells/m³ were found around the equator.In the last 60 years, the taxa number of phytoplankton community, including both Bacillariphyta and Dinophyta, increased.Dinophyta had higher species number than Bacillariophyta.However, Bacillariophyta always dominated phytoplankton community in the Eastern Indian Ocean, and the number of dominant species belonging to Chaetoceros spp. increased remarkably in the last several decades.