Recall that archaea and bacteria used to be grouped in the same category. how were archaeons first distinguished from other prokaryotes?

By difference in there ribosomal RNA sequence

Explanation:

Both bacteria and archaea lack membrane-bound nucleus and earlier both are considered in the same categories. Carl Woese was the scientist who discovered that bacteria and archaea are not similar.

Carl Woese and his lab members checked the ribosomal RNA in some archaeans and concluded that the archaeans are more closely related to eukaryotes than bacteria. After the study on archean Carl Woese classified the prokaryotes into two domains i.e., bacteria and archaea.  

Therefore by difference in the ribosomal RNA sequence archaeons first distinguished from other prokaryotes.