Sterols are unsaponifiable lipids from plant metabolism that exhibit interesting bioactive properties. Microalgae reveal a major source of specific phytosterols, most of them still not fully characterized. The similarity of sterol structure and the existence of positional isomers make it a great challenge in separation science. A method was developed based on offline two-dimensional (2D) system, reversed phase liquid chromatography (RPLC) ×  supercritical fluid chromatography (SFC)/quadrupole time-of-flight (Q-ToF) for the identification of sterols in microalgae. Subsequent positive-mode MS/MS was used to confirm the identified phytosterols. The 2D chromatogram revealed a pattern typical from the position of the unsaturations that was confirmed by standard injection, helping in the structural elucidation. The analysis of the unsaponifiable fraction of two algae, namely Scenedesmus obliquus a freshwater microalgae and Padina pavonica, a marine macroalgae, highlighted the ability of the method to distinguish a large number of sterol isomers.