During autumn 2007, an unusual increase in an algal species belonging to the order Prymnesiales was observed throughout the Baltic Sea Proper during routine national monitoring. Electron microscopical examination of the blooming species showed two types of flat scales - small and large - that resembled those of the alternate stage of Prymnesium polylepis. No spine-bearing scales were found. The 18S rDNA sequence data (n = 20, c. 1500 bp) verified the species identification as P. polylepis. There was up to 0.5% (7 bp) variability in the P. polylepis partial 18 S rDNA sequences from the Baltic Sea. These environmental sequences differed by 0-0.35% (0-4 bp) from cultured P. polylepis (isolate UIO036), and by 1.0-3.7% from other available Prymnesium sequences. The number of cells assumed to be P. polylepis began to increase in October 2007 coincidently with significantly calm and dry weather, and at their maximum the cells accounted for over 80% of the total phytoplankton biovolume in December-January. During February-April 2008, 95% of the Prymnesiales cells were in the size class of P. polylepis (>6 mu m). The species attained bloom concentrations (>1 x 10(6) cells l(-1)) from March to May 2008. The species was observed throughout the Baltic Sea, except the Bothnian Bay, Gulf of Riga and the Kattegat. No toxic effects of the bloom were observed.