Essentially the main difference between prokaryotes and eukaryote is that eukaryotes have compartmentalised organelles. This leads to major differences in their structure. Eukaryotes have a nucleus, with multiple chromosomes; Prokaryotes have a nucleoid region, with a singular chromosome and plasmids. Eukaryotes have a cell membrane; Prokaryotes have a cell membrane, cell wall and capsule (with flagella). Eukaryotes may contain chloroplasts and mitochondira; Prokaryotes do not.