Archae and bacteria are both Prokaryotes. Why are they group into two separate domain?
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Reducing your question to its fundamental misunderstanding
Similarly one could ask "Mammals and birds are vertebrates. Why are they grouped into two separate taxa?" (Bacteria and Archea include all procaryotes unlike my example). Or even better, one could ask "procaryotes and eukaryote are all alive. Why are they grouped into two separate taxa?" At the end of the day, your question boils down to
why do we group lineages together?.
Why do we group lineages together?
Population tend to diverge through time. For this reason we end up with a multitude of different lineages. As humans we can enjoy grouping lineages as we like to. One might group all yellow flowers together for example. However, a grouping which is of particular interest is one which represent evolutionary relationship. Insecta for example represents a group that include all currently living insects and all of their ancestors until the most recent common ancestor of all insects (that is the individual toward which all currently existing lineages coalesce). Such groups are called monophyletic.
You should have a look at this post where I made an intro to phylogenetic.
In short, to answer your question,
[W]hy are [Bacteria and Archea] grouped into two separate domain?
Because they represent two separate lineages.
Of course, different lineages often have distinct phenotypes which makes their grouping intuitive to a naturalist. For Bacteria and Archae, it takes some knowledge in molecular biology to tell how different they are phenotypically. This document from Colorado University does a good job in introducing the similarities and differences between Bacteria and Archae