All bacteria have peptidoglycans in the cell wall whereas the archaea do not. And what is seen only dimly, if at all, at higher levels of organization can be seen clearly at the level of molecular structure and sequences.
What's the difference between Archaea and Bacteria.Archaea have cell walls that lack peptidoglycan and have membranes that enclose lipids with hydrocarbons rather than fatty acids not a bilayer. I have a bio assignment and found a bit on how they're different. In the past, archaea were classified as bacteria and were called archaebacteria. But not all bacteria and archaea belong to prokaryotes. These lipids in the membranes of archaea are unique and contain ether linkages between the glycerol backbones rather than ester linkages. Though they were more similar to prokaryotes in structure.
Both also are different in RNA.Both bacteria and archaea have different Ribosomal RNAs rRNA. Both also are different in RNA polymerases and thus in their protein synthesis. Here is more information on the differences between these two microorganisms. Apart from their habitats, Bacteria and Archaea differ in cell wall structure and membrane lipid composition. There are two kinds of microorganisms that are divided into prokaryotes and those include bacteria and archaea. The similarities are that archaea and eubacteria are prokaryo.