The species composition and the biomass of intertidal microphytobenthos (MPB) were investigated at four sites in the Nakdong Estuary from Feb. to Dec. 2006. The chlorophyll (chl) ${alpha}$ concentration showed a positive correlation with MPB abundance, and depth profiles showed similar patterns: high at the surface, rapidly decreasing within 4 cm from the surface, and slowly decreasing thereafter. A MANOVA analysis revealed that the chl ${alpha}$ concentration varied significantly not only with depth, month, and site, but also with combinations of these factors. Among the four investigated sites, site D (Baekhabdeung) showed a seasonal biomass variation trend distinct from those of the other sites: higher in summer, decreased in autumn and with sustained low values until winter. As indicated, the other sites contrastingly showed low biomasses in summer, after which the biomasses continuously increased, with some variation among the sites. A cluster analysis of species composition indicated that sites near to each other and with similar sediment structures had closer similarities in the same seasons. The species of genus Amphora and Navicula were dominant at the four sites throughout the study period.