1. A 2-year (2002-2003) survey of chlorophyll and carotenoid pigments is reported for two off-shore stations of Lake Tanganyika, Kigoma (Tanzania) and Mpulungu (Zambia), and from three cruises between those sites. Chlorophyll a concentrations were low (0.3-3.4 mg m) and average chlorophyll a integrated through the 100 m water column were similar for both stations and years (36.4-41.3 mg m). Most pigments were located in the 0-60 m layer and decreased sharply downward. Chlorophyll a degradation products (phaeophytins and phaeophorbides) were detected at 100 m depth, whereas carotenoids became undetectable. Temporal and seasonal variation of the vertical distribution of pigments was high. 2. The biomass of phytoplankton groups was calculated from marker pigment concentrations over the 0-100 m water column using the CHEMTAX software. On average for the study period, chlorophytes dominated in the northern station, followed by cyanobacteria T1 (type 1, or Synechococcus pigment type), whereas cyanobacteria T1 dominated in the south. Cyanobacteria T2 (type 2, containing echinenone), presumably corresponding to filamentous taxa, were detected in the rainy season. Diatoms (and chrysophytes) developed better in the dry season conditions, with a deep mixed layer and increased nutrient availability. Very large variation in the vertical distribution of algal groups was observed. 3. Our observations on phytoplankton composition are broadly consistent with those from previous studies. Our pigment data provide evidence for the lake-wide importance of picocyanobacteria and high interannual variation and spatial heterogeneity of phytoplankton in Lake Tanganyika, which may render difficult assessment of long-term changes in phytoplankton driven by climate change.