One major difference between Domain Eukarya and Domains Bacteria and Archaea is the presence of a nucleus.

* Eukaryotic cells (Domain Eukarya) have a true nucleus enclosed within a membrane, where their genetic material (DNA) is stored.

* Prokaryotic cells (Domains Bacteria and Archaea) lack a nucleus. Their DNA is located in a region called the nucleoid, which is not enclosed by a membrane.