Eukaryotes are not classified as separate from prokaryotes when they form colonies of prokaryotes. Eukaryotes and prokaryotes are two distinct domains of life, characterized by fundamentally different cell structures and evolutionary histories. Prokaryotes are single-celled organisms that lack a membrane-bound nucleus and other membrane-bound organelles. In contrast, eukaryotes include all organisms with membrane-bound nuclei and organelles, encompassing a wide range of organisms from protists to animals, plants, and fungi.

When multiple prokaryotic cells coexist in close proximity or form colonial arrangements, they do not form eukaryotic cells nor constitute eukaryotes. These colonies or aggregates of prokaryotic cells still fall under the prokaryotic domain, as they maintain the structural and genetic traits characteristic of prokaryotes. Conversely, eukaryotic cells are distinct and distinct from prokaryotic colonies in terms of cellular complexity, cellular components, and evolutionary origins.