Columbus wrote in his logbook that on October 12, 1492, he used the royal flag, and that his captains used two flags which the admiral carried in all the ships as ensign, each white with a green cross in the middle and an 'F' and 'Y', both green and crowned with golden, open royal crowns, for Ferdinand II of Aragon and Ysabel (Isabel I).

[7] The independence movement in Puerto Rico gained momentum with the liberation successes of Simón Bolívar and José de San Martín in South America.

In 1868, Puerto Rican independence leader Ramón Emeterio Betances urged Mariana Bracetti to knit a revolutionary flag using the flag of the Dominican Republic as an example, promoting the then popular ideal of uniting the three Spanish-speaking Caribbean territories into an Antillean Confederation.

According to Puerto Rican poet Luis Lloréns Torres, the white cross on it stands for the yearning for homeland redemption; the red squares, the blood poured by the heroes of the rebellion and the white star in the blue solitude square, stands for liberty and freedom.

[11] In 1873, following the abdication of Amadeus, Duke of Aosta, as king (1870–1873) and with Spain's change from Kingdom to Republic, the Spanish government issued a new colonial flag for Puerto Rico.

Spain's flag once more flew over Puerto Rico with the restoration of the Spanish kingdom in 1873, until 1898 the year that the island became a possession of the United States under the terms of the Treaty of Paris (1898) in the aftermath of the Spanish–American War.

[16] Throughout Puerto Rico's political history various parties have designed and displayed flags representing their ideals.

The three main political parties of Puerto Rico are the New Progressive Party, which favors statehood and whose flag has what might resemble a blue palm tree inside a round cornered square in the middle with a white background; the Popular Democratic Party of Puerto Rico, flag has a red image of what is supposed to resemble a Puerto Rican jíbaro (farmer) in the middle with a white background; and the Puerto Rican Independence Party, whose flag has a white cross symbolizing Christianity and purity, on a green background which symbolizes hope.

Another political flag is that of the Boricua Popular Army, also known as Los Macheteros, an underground pro-independence group which believes and has often resorted to the use of violence.

The standard representative symbol carried by Puerto Ricans at international sports events, such as the Olympics, Pan American Games, Central American and Caribbean Games, and the World Cup of Baseball, is the current flag of Puerto Rico.