The domain of archaea represents a group of organisms which are only distantly related to the bacteria and eukaryotes. The classification of living organism into the three domains bacteria, archaea and eukaryotes has been introduced by Carl Woese and was based on comparison of 16S rRNA sequences (Woese et al., 1990, Woese & Fox, 1977). Sequencing and comparison of the genetic information of organisms determines the degree of differences between them and therefore is an indication of the amount of changes undergone by each species from a shared evolutionary ancestor. The ribosome is an essential part of the protein synthesis machinery and therefore the comparison of the 16S rRNA components of ribosomes gives a reliable picture of evolution and classification of species. Furthermore, 16S rRNA is extracted relatively simple and from every cell in high amounts. However, the acceptance of archaea as the third domain of life has been challenging due to the fact that both bacteria and archaea lack a nucleus and the morphology of both organismic groups appears similar. Despite the minimal morphological differences, bacteria and archaea do differ in information processing, DNA transcription, post translation modification of proteins and the assembly of flagella.