Why did Puerto Rico and San Juan switch names?
The first Governor of Puerto Rico, Juan Ponce de Leon, changed the name. He prefered that way. The actual name of the Island those time was San Juan Bautista, and the Capital was name Puerto Rico for the huge port back then.
Puerto Rico was named by the Taino people, Boriken, (Borinquen), When the spaniards arrived to the island they named it San Juan Bautista(Saint John the Baptist), and the capital, Puerto Rico, then later on the names got switched, the island Puerto Rico, and the capital, San Juan Bautista, San Juan for short.