There is only limited information about the accumulation of algal toxins in aquatic organisms in the Baltic Sea. In this study we measured total cyanobacterial hepatotoxin levels in blue mussel (Mytilus edulis) and flounderi (Platichthys flesus) tissues. Flounder were caught with gillnets from the western Gulf of Finland during July and August 1999. Blue mussels were collected from an enclosure at 3 m depth and from an artificial reef (wreck, 25-35 m depth) in the western Gulf of Finland between June and September 1999. Flounder liver and muscle samples and soft tissues of mussels were analyzed for the cyanobacterial hepatotoxins (nodularin, NODLN and / or microcystins, MCs) using an enzyme-linked immunosorbent assay (ELISA). Results showed a time-dependent accumulation of hepatotoxins in flounder and mussels. In flounder, the maximum concentration 399 ± 5 (sd) ng NODLN or MC/g dry weight (dw) was found in the liver of specimens caught on 21 August 1999. No hepatotoxins were detected in muscle samples. The maximum concentration of 2150 ng ± 60 (sd) ng hepatotoxin/g dw was found in the mussel soft tissues collected on 20 August 1999. Temporal NODLN or MC trends indicated depuration of cyanobacterial hepatotoxin from mussels at surface level and an increase in NODLN or MC concentrations in those from the sea bed. These studies showed that despite the low cyanobacteria cell numbers the cyanobacterial hepatotoxins can accumulate in flounder and mussels. This may allow the further transfer of cyanobacterial hepatotoxins in the food web.