Ribosomal RNA is a molecular building block for ribosomes. Under this system, organisms are classified into three domains and six kingdoms. The domains are Archaea, Bacteria, and Eukarya. The kingdoms are Archaebacteria (ancient bacteria), Eubacteria (true bacteria), Protista, Fungi, Plantae, and Animalia.The Archaea and Bacteria domains contain prokaryotic organisms.he Three Domain System, developed by Carl Woese, is a system for classifying biological organisms. Over the years, scientists have developed several systems for the classification of organisms.