| Summary: | The dinoflagellates Gymnodinium corollarium (Gc), Biecheleria baltica (Bb), and Apocalathium malmogiense (Am) are very difficult to separate using traditional light microscopy. Their dominance patterns may have ecosystem-wide consequences in terms of, e.g., the Baltic Sea carbon cycle. This study describes a protocol to separate them, determines their relative abundances, and suggests the adjustment of monitoring programs. A relatively simple staining technique was found to be suitable to identify Gc, Bb, and Am. Opposite trends were observed for Gc (increasing) and Bb (decreasing) along with the spring bloom, indicating different niches. Two clusters of sub-basins were identified: 1) almost absolute dominance of the usually grouped biomass by Gc; and 2) Bb also became dominant. Gc occasionally dominated even the overall microscopy-derived biomass, Bb clearly contributed, and Am contributed minor proportions. The proposed strategy can be implemented in monitoring protocols. This will facilitate the tracking of changes within Baltic Sea phytoplankton assemblages.
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