The phytoplankton standing crop was assessed in detail along the South Eastern Arabian Sea (SEAS) during the different phases of coastal upwelling in 2009. During phase 1 intense upwelling was observed along the southern transects(8°N and 8.5°N). The maximum chlorophyll <i>a</i> concentration (22.7 mg m<sup>-3</sup>) was observedin the coastal waters off Thiruvananthapuram (8.5°N). Further north there was no signature of upwelling, with extensive <i> Trichodesmium erythraeum</i> blooms. Diatoms dominated in these upwelling regions with thecentric diatom <i> Chaetoceros curvisetus</i> being the dominant species along the 8°N transect. Along the 8.5°N transect pennate diatoms like <i> Nitzschia seriata</i> and <i>Pseudo-nitzschia</i> sp. dominated. Duringphase 2, upwelling of varying intensity was observed throughout the study area with maximum chlorophyll <i>a</i> concentrations along the 9°N transect (25 mg m<sup>-3</sup>) with <i> Chaetoceros curvisetus</i> as the dominantphytoplankton. Along the 8.5°N transect pennate diatoms during phase 1 were replaced by centric diatoms like <i>Chaetoceros</i> sp. The presence of solitary pennate diatoms <i>Amphora</i> sp. and <i> Navicula</i> sp.were significant in the waters off Kochi. Upwelling was waning during phase 3 and was confined to the coastal waters of the southern transects with the highest chlorophyll <i>a</i> concentration of 11.2 mg m<sup>-3</sup>. Along withdiatoms, dinoflagellate cell densities increased in phases 2 and 3. In the northern transects (9°N and 10°N) the proportion of dinoflagellates was comparatively higher and was represented mainly by <i>Protoperidinium</i> spp