Extracts from seawater and sediment pore water samples were characterised by capillary electrophoresis (CE). Siderophores of the ferrioxamine family were identified. Ferrioxamine E is the dominant siderophore in both seawater and sediment pore water samples from different regions of the Baltic Sea. Ferrioxamine G was identified in subsurface seawater samples from the Gdansk Deep. Rhodotorulic acid was also identified in seawater samples from the euphotic zone (0-30 m) of Puck Bay and in sediment pore water from Puck Bay and the Bornholm Deep. Ferrioxamine B was not found. The presence of catechol siderophores was not investigated.