The flag state of a merchant vessel is the jurisdiction under whose laws the vessel is registered or licensed, and is deemed the nationality of the vessel. A merchant vessel must be registered and can only be registered in one jurisdiction, but may change the register in which it is registered. The flag state has the authority and responsibility to enforce regulations over vessels registered under its flag, including those relating to inspection, certification, and issuance of safety and pollution prevention documents. As a ship operates under the laws of its flag state, these laws are applicable if the ship is involved in an admiralty case.

The term "flag of convenience" describes the business practice of registering a merchant ship in a state other than that of the ship's owners, and flying that state's civil ensign on the ship. Ships may be registered under flags of convenience to reduce operating costs, or else to avoid the regulations of, or inspection and scrutiny by, the country of the original owner. Normally the nationality (i.e., flag) of the ship determines the taxing jurisdiction.

Since the Flag Right Declaration of 1921, it has been recognised that all states—including land-locked countries—have a right to maintain a ship register and be a ship's flag state. Because of the failure of some flag states to comply with their survey and certification responsibilities, especially flag-of-convenience states that have delegated their task to classification societies, a number of states have since 1982 established port state controls of foreign-registered ships entering their jurisdiction.

As at January 2010, Panama was the world's largest flag state, with almost a quarter of the world's ocean-going tonnage registered there. The United States and the United Kingdom had only about 1% each.