Protists are unicellular eukaryotes, whereas Eubacteria and Archaebacteria are unicellular prokaryotes.
Eubacteria and Archaebacteria belong to kingdom Monera; whereas Protists belong to kingdom Protista.
All Monerans have prokaryotic cell structure. Protists have eukaryotic cell structure and are unicellular.
Protists either lack cell wall or have cell wall made up of cellulose.
Eukaryotes have cell wall made up of peptidoglycan or murein.
In Archaebacteria cell wall lacks peptidoglycan but contains proteins and non-cellulosic polysaccharides.
Protists have typical sexual reproduction involving fusion of gametes. In Eubacteria and Archaebacteria typical sexual reproduction is absent.
Cell division is mitotic type in Protists and amitotic in Eubacteria and Archaebacteria.
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