Archaea have been relatively recently classified as a Domain of life that had previously been lumped in with Bacteria. They had been named "archaebacteria", but have since been found to be significantly different than Bacteria. The uniqueness of their genetics, metabolism, and biochemistry are now recognized as reason to set them apart.
Only 8 of the estimated 23 phyla have been cultured and studied so far, and many of these have been found in extreme environments (acidic and extreme thermal conditions, etc.). This fascinating group of organisms are in need of a lot of study.