: This article describes the design and the synthesis of two analogues of archaeal bipolar lipids that differ only by the configuration of a single stereogenic centre on a glyceryl moiety. The corresponding comparative physicochemical study by tensiometry/ellipsometry and atomic force microscopy provided a set of data that points out the effect of this single stereochemical variation. The two epimers revealed different conformations at the air/water interface resulting in a more or less tendency for a bent or a stretched conformation. It strengthens the importance of the stereochemistry in such bipolar lipid packing.