Here we report the lipid profiles of ten dinoflagellate species originating from different freshwater habitats and grown at 4, 13 or 20°C akin to their natural occurrence. Lipids were determined by High Performance Liquid Chromatography-ElectroSpray Ionization-Mass Spectrometry in positive and negative ion modes. Besides the well-studied monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) lipids, our study revealed the presence of intact molecular lipid species of trigalactosyldiacylglycerols (TGDG), betaine diacylglyceryl-carboxyhydroxymethylcholine (DGCC), sulfolipid sulfoquinovosyldiacylglycerols (SQDG) and phospholipids, in particular phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylglycerol (PG).In multivariate ordination, the freshwater dinoflagellates studied could be distinguished into two groups based on their lipid profiles. Peridinium aciculiferum, Borghiella dodgei, B. tenuissima and Tovellia coronata belonged to group 1 while Ceratium cornutum, Gymnodinium palustre, Jadwigia applanata, P. cinctum, P. willei and P. gatunense belonged to group 2. Indicator species analysis evidenced that group 1 was characterized by 36:9 MGDG and 36:9 DGDG and group 2 by 38:9 and 38:10 MGDG, 38:9 and 38:10 DGDG and 34:1 SQDG. We suggest that the grouping of dinoflagellates indicated their range of temperature tolerance. Furthermore, non-thylakoid lipids were linked to dinoflagellate phylogeny based on the large ribosomal sub-unit (28S LSU) rather than their temperature tolerance. Thus certain lipids better reflected habitat adaptation while other lipids better reflected genetic diversity
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