Ocean-related global changes have altered phytoplankton community structure, especially the diatom-dinoflagellate competition, which further influences ecosystem structure and functions. The pivotal ecological roles of diatoms and dinoflagellates are strongly related with their biochemical composition, but quantitative comparisons of biochemical changes between diatoms and dinoflagellates under variable environments are still limited. We investigated responses of lipid biomarkers (sterols and fatty acids (FAs)) to different temperatures (12, 18 and 24 °C), nitrogen and phosphorus concentrations and their molar ratios (N:P ratios) of 10:1, 24:1 and 63:1 in marine diatom Phaeodactylum tricornutum and dinoflagellate Prorocentrum minimum. Over these wide ranges of temperature and nutrient conditions, sterol and FA profiles were relatively stable in the two species. For carbon-normalized contents of major lipid biomarkers, warming caused non-significant changes in the diatoms but an increase (up to 153%) in the dinoflagellates. Eutrophication caused an overall decrease (up to 53%) in major lipid biomarker contents in the diatoms but an overall increase (up to 77%) in the dinoflagellates. In contrast, imbalanced N:P ratios caused an overall increase (up to 64%) in major lipid biomarker contents in the diatoms but an overall decrease (up to 53%) in the dinoflagellates. Taken together, our results showed that the contents of major sterols and polyunsaturated FAs would change non-significantly in the diatom P. tricornutum, while those in the dinoflagellate P. minimum would increase (ca. 9–48%) under future ocean warming, eutrophication and imbalanced N:P ratios. This study expands our knowledge on lipid-based indicators of phytoplankton under changing environments, which by systematically linking with several other aspects of food quality will help to understand ecological consequences of diatom-dinoflagellate community changes. [ABSTRACT FROM AUTHOR]