Compare and contrast the six-kingdom system of classification with the three-domain system. What evidence prompted the development of the three-domain system? The three-domain system has Archaea, Bacteria, and Eukarya. The six kingdoms are Eubacteria, Archaebacteria, Protista, Fungi, Plantae, and Animalia. New evidence revealed that the two main prokaryote groups are even more different from each other than eukaryotes. Therefore, scientists established the domain system.