We studied the vertical structure of the phytoplankton community in two toxic cyanobacterial blooms in the offshore Baltic Sea. In 1994, vertically separated potentially toxic, diazotrophic and mixotrophic species (belonging to Cyanophyceae, Dinophyceae and Pryinnesiophyceae) dominated. In 1997, picocyanobacteria, mainly in colonies, made up 40-50% of the total phytoplankton carbon biomass in the top 20 m both day and night. Colony-forming species of picocyanobacteria seem to be occasionally important and hitherto underestimated in the Baltic Sea. We found species-specific depth distribution patterns. Nodularia spumigena and Anabaena spp. were observed mainly above 10 in depth, while Aphanizomenon sp. was mostly found deeper, especially at night. Dinophysis norvegica was only abundant near the seasonal pycnocline and showed very limited diurnal migration. Other flagellates, including small Cryptophyceae and 10 identified Chrysochromulina species, occurred down to 40 m depth. Their vertical migration may help to retrieve nutrients from below the summer pycnocline. We conclude that considerable differences in dominating functional groups may occur between years/bloom stages, and that the vertical distribution pattern of many species is recurring at similar environmental conditions, suggesting species-specific niche-separation. (c) 2006 Elsevier B.V. All rights reserved.