Over the years, the term "flagship" has become a metaphor used in industries such as broadcasting, automobiles, airlines, and retailing to refer to their highest profile or most expensive products and locations.
In common naval use, the term flagship is fundamentally a temporary designation; the flagship is wherever the admiral's flag is being flown. However, admirals have always needed additional facilities, including a meeting room large enough to hold all the captains of the fleet and a place for the admiral's staff to make plans and draw up orders. Historically, only larger ships could accommodate such requirements.
The term was also used by commercial fleets, when the distinction between a nation's navy and merchant fleet was not clear. An example was Sea Venture, flagship of the fleet of the Virginia Company, which was captained by Royal Navy Vice-Admiral Christopher Newport yet bore the Merchant Navy admiral of the company's fleet, Sir George Somers, during the ill-fated Third Supply of 1609.
In the age of sailing ships, the flagship was typically a first rate; the aft of one of the three decks would become the admiral's quarters and staff offices. This can be seen on HMS Victory, the flagship of Admiral Nelson at the Battle of Trafalgar in 1805, still serving the Royal Navy as the ceremonial flagship of the First Sea Lord from Portsmouth, England. Non-first rates could serve as flagships, however: USS Constitution, a frigate (a fifth rate), served as flagship for parts of the United States Navy during the early 19th century.
In the 20th century, ships became large enough that the larger types, cruisers and up, could accommodate a commander and staff. Some larger ships may have a separate flag bridge for use by the admiral and his staff while the captain commands from the main navigation bridge. Because its primary function is to coordinate a fleet, a flagship is not necessarily more heavily armed or armored than other ships. During World War II admirals often preferred a faster ship over the largest one.