Archaebacteria differ from eubacteria in cell membrane structure.

The most significant difference is in the lipids that make up their cell membranes. Eubacteria have cell membranes primarily composed of phospholipids with fatty acids linked by ester bonds. In contrast, archaebacteria have cell membranes made up of ether-linked lipids composed of isoprenoid hydrocarbons. These unique lipids make archaeal cell membranes more stable and resistant to environmental extremes.