Four in situ incubation experiments were conducted in May, August and November 2009, as well as February 2010 to determine the seasonal primary productivity and the community structure of phytoplankton at the Seomjin estuary. The primary production of phytoplankton ranged from 9 to 3560 mgC m-2 d-1. Primary productivity was the highest in the summer season (August), which was influenced by improved optical and temperature conditions of the water, as well as the supply of nutrients derived from its surrounding watershed. Particularly, the upper station (SJ-1, SJ-2) of Seom-jin estuary showed a higher productivity, as a result of inflow of input nutrients originated from the terrestrial source. The fucoxanthin, as an index pigment of diatoms showed the highest concentration (0.74~9.51 μg L-1) at all stations, occupying 30~80% to total Chl a concentrations. The phytoplankton species composition determination, using a microscope showed similar results to the pigment analysis, which indicated diatom Skeletonema costatum, as the dominant species. The primary productivity in Seom-jin estuary indicates temporally and spatially large variation, according to different environmental conditions. Also, Skeletonema costatum has euryhaline features with relatively higher contribution.