The placement of prokaryotes into major clades within the domains Archaea and Bacteria has been based on .

Molecular evidence

Explanation:

Earlier archaea were considered as bacteria because they show some similarities with bacteria like binary fission as mode of reproduction, lack of a nucleus, etc.

Later Carl Woese separated bacteria in a different domain and divide prokaryote into two domains called bacteria and archaea. He separated archaea from bacteria on molecules evidence.

He compaired rRNA sequence between bacteria and archaea and observed that they both differ in rRNA sequence which allowed him to make a separate domain for archaea.