When the crew found the settlement in San Sebastian in ruins, Balboa persuaded them to go to a region known as Darien, in what is now Panama. There they founded a new colony. When the leaders of the settlement quarreled, Balboa took command. Soon after, he set out to conquer nearby territory. Balboa used brutal tactics to defeat the Native Americans living on neighboring lands.

On one of his expeditions, Balboa heard from an Indian chief about a great ocean on the other side of the mountains and of the gold to be found there. Balboa sent word to Spain that he needed more people to help him explore the area. The government organized a large expedition, but Balboa was not put in charge. Instead, the king named nobleman Pedro Arias Dávila commander and governor of Darien. The expedition left Spain in 1514.

Balboa, however, had already taken action. Without waiting for reinforcements, he set out in September 1513 to cross the Isthmus of Panama—that is, the narrow strip of land joining Central and South America. Balboa and his party of 190 Spaniards and 1,000 Native Americans cut their way through dense jungle and climbed across mountains. When they reached the top of the last range they saw before them a vast expanse of sea. The body of water they discovered was the Pacific Ocean. Balboa called it the South Sea. He claimed the ocean and all lands washed by it in the name of Spain.

When news of the discovery reached the king, Balboa was named governor of the South Sea. However, he remained subject to the authority of Pedro Arias Dávila, the governor of Darien. When Balboa returned to Darien, conflict arose between him and the governor. Balboa was eventually allowed to explore the South Sea. Later, however, he was summoned back to Darien and charged with rebellion, treason, and other crimes. He was found guilty and executed in January 1519.