Abstract The distribution and composition of phytoplankton assemblages were studied in the Gerlache and Bransfield Straits (Antarctic Peninsula) during the FRUELA 95 (December 1995) and FRUELA 96 (January 1996) cruises, using light microscopy and HPLC pigment analysis. Based on phytoplankton size and composition, two regions could be distinguished. The first region embraced the southwestern part of the Gerlache Strait, including a frontal system in the northeastern area. Chlorophyll (Chl) a values were generally high in surface waters (from 3.5 to 26.2 μg l−1). Phytoplankton assemblages in the stratified waters of the southwestern Gerlache Strait were dominated by large diatoms and the flagellate Pyramimonas sp. (mixed with Phaeocystis in FRUELA 95). Pigment patterns included Chl a, Chl b, different Chls c, and fucoxanthin as the major carotenoid. The frontal zone was characterized by a bloom of Pyramimonas. Following a transect from southwestern Gerlache Strait towards the Bransfield Strait an increased contribution of Chl b, violaxanthin, and two unknown carotenoids (tentatively identified as loroxanthin and loroxanthin-ester) was observed which paralleled the Pyramimonas distribution. The marker pigment lutein, usually associated with chlorophytes and prasinoxanthin-lacking prasinophyceans, was only detected at very low concentrations. The second region, embracing the Bransfield Strait and one station in the Drake Passage, was characterized by stratified waters and low Chl a concentration (from 0.18 to 3.88 μg l−1). Phytoplankton assemblages were dominated by the nanoplankter Cryptomonas sp. (FRUELA 95), the colonial haptophyte Phaeocystis cf. antarctica, and small flagellates (FRUELA 96). Pigment composition was mainly constituted by Chl a, Chl c2, Chl c3, alloxanthin, fucoxanthin, 19′-butanoyloxyfucoxanthin, and 19′-hexanoyloxyfucoxanthin. HPLC pigment data were processed using a factorization matrix program (CHEMTAX) to estimate the contribution of different algal classes to total Chl a. Four ‘algal groups’ were included in the chemotaxonomic approach: ‘diatoms’, ‘Phaeocystis’, ‘cryptophytes’, and ‘Pyramimonas’. A fifth ‘chemotaxonomic group’ was defined to reconstruct the distribution of an assemblage consisting of autotrophic peridinin-lacking dinoflagellates, some haptophytes, and chrysophytes, which were probably included by cell counting into the single group of ‘small flagellates’. The distribution patterns of the CHEMTAX groups were in agreement with cell counts of diatoms, cryptophytes, and Pyramimonas. Discrepancies were observed for P. cf. antarctica as well as for small flagellates and dinoflagellates. Significant positive correlations were found between phytoplankton cell counts and different Chls c, suggesting the chemotaxonomic usefulness of Chls c as marker pigments for phytoplankton groups in addition to carotenoids.