Measurements of the stress imposed by a PSII inhibiting herbicide (Irgarol 1051) on the composition of a phytoplankton community was investigated by comparing chemotaxonomy, as determined by high performance liquid chromatography (HPLC), optical microscopy and analytical flow cytometry (AFC). Changes in community structure were induced in microcosms containing a natural marine phytoplankton community exposed to different concentrations of Irgarol 1051 (0.5 and 1.0 microgl-1). Microcosms were maintained under controlled laboratory conditions in semi-continuous culture over 120 h. Class-specific phytoplankton biomass (chlorophyll a) was estimated using CHEMTAX analyses of pigment concentrations. Microscopic identification and carbon content estimates were cross-correlated with CHEMTAX and also with AFC enumeration/size classifications of major phytoplankton groups. CHEMTAX-HPLC analyses and microscopy results demonstrated that prasinophytes and prymnesiophytes were the most affected groups following exposure to Irgarol 1051. The selective reductions in both classes as estimated by both techniques revealed similar trends. Results for chlorophytes and dinoflagellates showed these groups to be most tolerant to Irgarol 1051. Indeed, class-specific biomass for chlorophytes as determined by CHEMTAX and microscopy were correlated (R2=0.53) which demonstrated an increase in both abundance and carbon content following exposures to Irgarol 1051. Abundances of nanoeukaryotes as determined by microscopy afforded good agreement with results from AFC (R2=0.8), although for picoeukaryotes, abundances were underestimated by microscopy (R2=0.43). The relative performance of the selected techniques is discussed.