Prokaryotes are divided into two different kingdoms; Bacteria and Archaea. The major comparison between them is:
Cell wall of bacteria is made up of peptidoglycans, while that of archaea is composed of pseudomureins.
Bacteria have one rRNA while archaea have three rRNA.
Growth of bacteria can be inhibited by antibiotics while that of archaea can't be inhibited by antibiotics.
Bacteria can't survive at extreme high temperature above 100 degree Celsius, while archaea can survive in both extreme physical and geological conditions.