The results of differences in phytoplankton pigments composition are presented in this paper. Samples from the Southern Baltic taken during three cruises on r/v ?Oceania? (14.02 - 28.02.2000, 06.05 - 16.05.2000 and 20.09 - 01.10.2000) were examined. Qualification and quantification analyses of chlorophylls and carotenoids present in samples of naturally existing phytoplankton were based on the RP-HPLC technique. Seasonal and spatial variability in pigment characteristics was observed in the analysed seasons. Presence of: chlorophyll a, chlorophyll c1+c2, chlorophyll b, alloxanthin, zeaxanthin, fucoxanthin, peridinin, neoxanthin, diadinoxanthin - was noted in every season; violaxanthin and beta-carotene - only in May and September. Lutein was detected only in May samples. The quantity of May and September pigments exceeded 2-6 times the February pigments content. Vertical differentiation in the pigments amount was also noted. Spatial variability emphasized the influence of Vistula and Odra water masses. Different markers of phytoplankton species were found in each season: in February - cryptophytes (alloxanthin), May - diatoms (fucoxanthin) and September - cyanophytes and dinophytes (containing zeaxanthin and diadinoxanthin).