Independent agencies can be distinguished from the federal executive departments and other executive agencies by their structural and functional characteristics. Congress can also designate certain agencies explicitly as "independent" in the governing statute, but the functional differences have more legal significance.
While most executive agencies have a single director, administrator, or secretary appointed by the President of the United States, independent agencies almost always have a commission, board, or similar collegial body consisting of five to seven members who share power over the agency. (This is why many independent agencies include the word "Commission" or "Board" in their name). The President appoints the commissioners or board members, subject to Senate confirmation, but they often serve with staggered terms, and often for longer terms than a usual four-year Presidential term, meaning most Presidents will not have the opportunity to appoint all the commissioners of a given independent agency. Normally the President can designate which Commissioner will serve as the Chairperson. Normally there are statutory provisions limiting the President's authority to remove commissioners, typically for incapacity, neglect of duty, malfeasance, or other good cause. In addition, most independent agencies have a statutory requirement of bipartisan membership on the commission, so the President cannot simply fill vacancies with members of his own political party.