The Lighthouse is the only building which is not built on your island, but on a rock in the sea. Therefore it's prebuilt, but throughout the game you'll have several opportunities to upgrade it.
The higher the level your Lighthouse is on is, the more ship points you get and the more ships you can build. Furthermore, the Lighthouse serves as a "parking place" for your ships, i.e. when they're idle, they will stay around the Lighthouse.
More ship points can be purchased by using rubies or ducats.
The Lighthouse changes appearance when it's upgraded to higher levels.