A flagship is a designation to a certain Capital Ship. If you only have one Capital Ship, it is automatically designated as a Flagship. If an empire has multiple Capital Ships, the "Flagship" designation is given to your highest level Capital Ship. If two capital ships are tied for highest level, neither receive the designation. The Flagship status has no effect on a ship's abilities or combat performance. Flagships can be any type of Capital Ship, most of the time getting a Flagship is considered pointless, as all Capital Ships will reach the same level eventually, and its not very tactical to train one ship more than others. When in a fleet, the Flagship of that fleet (the ship selected when you make the fleet) is its center, other ships will flock around it. this type of flagship does not need to be the highest level.