When archaebacteria evolved from a common monera ancestor, they became the first branching of the evolutionary tree.
Later, the archaea group branched again;
some archaea developed into archaebacteria, while others form the plant, animal, protest and fungi life we know today.
For one thing, unlike bacteria, archaea have a genetic makeup that resists antibiotics. Furthermore, archaea lack segments of genes known as introns, which regulate gene expression. Archaea and the eukaryotes evolving from them have more complex RNA than their bacterial relatives. In addition, the structures of archaean and bacterial cell walls are very different; unlike bacteria, archaea use no peptidoglycan in their cell walls. Morever, archaean and bacterial membranes are made up different types of membrane lipids. Because of these basic differences, archaea and bacteria are considered as separate domains.