Both bacteria and the archaea possess distinct Ribosomal Nucleic Acids (rRNA). Archaea do have three RNA polymerases, just like eukaryotes, but the bacteria only possess one. Archaea do have cell walls that lack peptidoglycan, and they also do have membranes that enclose lipids with hydrocarbons instead of fatty acids.
These lipids that are in the membranes of archaea are unique, and they contain linkages that lie between the glycerol backbones instead of ester linkages. Archaea share a resemblance with eukaryotes than bacteria. Their ribosomes also work more like the eukaryotic ribosome more than bacterial ribosomes.
Both microorganisms differ in both genetic and biochemical ways. Only in the last decades ago, archaea were recognized as a very distinct domain of life. They are extremophiles, which means they thrive in very extreme conditions. They also have similar ecological roles as bacteria. Both of these organisms respond to various antibiotics in a very different manner.