Vertical distribution of a phototrophic ciliate ( Mesodinium rubrum), autotrophic dinoflagellates ( Peridiniella catenata, Heterocapsa rotundata, Dinophysis acuminata), a cryptomonad ( Teleaulax sp.), a filamentous cyanobacterium ( Aphanizomenon flos-aquae), a non-motile chlorophyte ( Monoraphidium sp.) and two heterotrophic dinoflagellates were studied during two diel periods in spring (May 1–2 and 27–28, 1995) and summer (June 26–27 and July 6–7, 1994) in the southern part of the Gulf of Riga, the Baltic Sea. The two seasons, corresponding to the vernal bloom and summer stage, differed considerably with respect to phytoplankton community, hydrography and vertical distribution of the species. In spring the cells stayed in the upper mixed layer above a strong thermocline at 12–15 m depth, and changes in the vertical distribution were related to surface avoidance in the middle of the day. By using correspondence analysis, the vertical distribution of all the motile species were shown to differ significantly from the non-motile Monoraphidium, but not from each other. The vertical migration was reflected in a higher variability in the depth distribution patterns of the motile species, compared to Monoraphidium. In summer 1994, Aphanizomenon, Dinophysis and Teleaulax showed similar depth distribution patterns during the first period, but different from Mesodinium and the heterotrophic dinoflagellates, while during the second period all the autotrophic species had a species specific depth distribution pattern. Me. rubrum revealed a considerably different depth distribution between the two seasons, characterised by surface accumulation in spring and relatively uniform depth distribution over the whole sampling range (0–30 m) in summer. The results demonstrate different vertical niche separation strategies between species.