There are four main differences; 1. DNA - Eukaryotes have linear DNA whereas prokaryotes have circular DNA. The DNA in eukaryotes is also protien bound, this is not the case in prokaryotes. 2. Organelles - Eukaryotes have membrane bound organelles including a nuclues, prokaryotes do not have a nucleus or any other membrane bound organelles. 3. Reproduction - Eukaryotes use meiosis or mitosis to reproduce, prokaryotes use binary fission 4. Size - Generally eukaryotes are bigger in size than prokaryotic organisms.