Some Archaeal organisms, now known to be the halophiarchaea, have been known for more than 20 years. His arguments for the uniqueness of the Archaeal organisms included their specific genetic motifs, and other certain specific molecular features that set them apart from both bacteria and eukaryotes. Although there is some continued debate, the decision to maintain a defined archaeal domain is holding up pretty well.
Some people feel that they are closely related to bacteria.
It is true that they do contain many bacterial genes. To many people it is a question of where you draw the line. The mix of archaeal molecular features are common to all Archaea. Examples of these include their rRNA, and their RNA polymerase. Their way of carrying out transcription is actually most closely related to that of eukaryotic cells.