ABSTRACT. Measurements of natural estuarine microphytobenthos communities were carried out in samples of intertidal sedlrnents of the Tagus Estuary (Portugal) by means of pigment analysis by HPLC in order to identify microphytobenthos composition. The relative abundance of taxa was determined by microscopic observations. During spring 16 sites were sampled and 3 of them, differing in sediment grain size and tidal level, were, \ isited fortnightly for 1 yr. At all sites throughout the year, diatoms were the dominant algal group, evidenced by the. relatively high concentrations of chlorophylls cI+c2, fucoxanthin, neofucoxanthin, diadinoxanthin, diatoxanthin and 0-carotene. Chl b and diatoxanthin were related with observed euglenophyte populations, zeaxanthin with cyanobacteria, lutein with macrophyte debris and alloxanthin with falling phytoplanktonic cells of cryptophytes. The spatial study allowed a distinction between sites regarding the presence of macrophyte debris, euglenophytes or only diatolns. The temporal survey showed the seasonal trends of diatoms and cyanobacteria and the main periods of plant debris deposition. Pheophytin a and chlorophyllide a concentrations were quite low. Degraded chloropigments were constituted mainly of pheophorbides a, 9 of which were quantified. The most abundant among them indicated intensive grazing by ~nacrozoobenthos at the muddy stations.