The main difference between eminent domain and adverse possession is that eminent domain is initiated by the government, while adverse possession is initiated by a private individual. Eminent domain is used for public purposes and requires that the government compensate the owner of the property, while adverse possession is a way for someone to obtain ownership of property without paying for it. Additionally, eminent domain involves taking the entire property, while adverse possession only involves taking ownership of the portion of the property that the claimant has been using.