There are several major differences between the structures of the prokaryotic cell from that of the eukaryotic cell.
| Basis of differentiation | Prokaryotic cell structure | Eukaryotic cell structure |
| Cell type | Unicellular | Mostly multicellular with the exception of yeasts and algae which are unicellular |
| Size | Smaller - size range from 0.1 μm - 5 μm | Larger – size ranges from 10 μm -100 μm |
| Cell wall | Usually present, chemically complex in nature and forms the outermost layer of the cell | Only present in plant cells as the outermost layer, is chemically simple in nature – absent in animal cells |
| Capsule | An outer protective covering found only in the bacterial cells, in addition to the cell wall | Absent |
| Cell membrane | Surrounds the cytoplasm and regulates the entry and exit of substances in the cells | Surrounds the cytoplasm, separating the cell from the outside environment and aiding in the exchange of substances in and out of the cell. |
| Ribosomes | Smaller in size and spherical in shape | Comparatively larger in size and linear in shape |
| Nucleus | Absent – has a nucleoid instead, which is simply a central region of the cell that contains its DNA | Has a true, membrane-bound nucleus |
| DNA form | Single DNA in circular arrangement | DNA in linear arrangement |
| Mitochondria | Absent | Present |
| Endoplasmic Reticulum | Absent | Present |
| Plasmids | Present | Very rarely found |
| Lysosomes and centrosomes | Absent | Present |
| Cytoplasm | Present, but cell organelles absent | Present, cell organelles present |
| Flagella | Smaller in size | Larger in size |