The dispute continued for some time.  Medical certificates were presented declaring Caparra unhealthy.  The leading inhabitants declared their opinion in favor of the transfer.  A petition was signed and addressed to the Jerome friars, who governed in la Espanola, and they ordered the transfer in June, 1519.  Ponce was permitted to remain in his stone house in the abandoned town as long as he liked.  In November, 1520, Castro wrote to the emperor expressing his satisfaction with the change, and asked that a fort and a stone smelting-house might be constructed, because the one in use was of straw and had been burned on several occasions.  Finally, in 1521, the translation of the capital of Puerto Rico to its present site was officially recognized and approved.

There were now two settlements in the island.  There were 35 citizens in each in 1515, but the gold produced attracted others, and in 1529 the Bishop of la Espanola reported that there were 120 houses in San Juan, “some of stone, the majority of straw.  The church was roofed while I was there.”  He says, “a Dominican monastery was in course of construction, nearly finished, with more than 125 friars in it.”

During the next five years the gold produce rapidly diminished; the Indians, who extracted it, escaped or died.  Tempests and epidemics devastated the land.  The Caribs and the French freebooters destroyed what the former spared.  All those who could, emigrated to Mexico or Peru, and such was the depopulated condition of the capital, that Governor Lando wrote in 1534:  “If a ship with 50 men were to come during the night, they could land and kill all who live here.”

With the inhabitants engaged in the cultivation of sugar-cane, some improvement in their condition took place.  Still, there were only 130 citizens in San Juan in 1556, and only 30 in New San German.  In 1595, when Drake appeared before San Juan with a fleet of 26 ships, the governor could only muster a few peons and 50 horsemen, and but for the accidental presence of the Spanish frigates, Puerto Rico would probably be an English possession to-day.  It was taken by the Duke of Cumberland four years later, but abandoned again on account of the epidemic that broke out among the English troops.  When the Hollanders laid siege to the capital in 1625 there were only 330 men between citizens and jibaros that could be collected for the defense.  In 1646 there were 500 citizens and 400 houses in San Juan, and 200 citizens in New San German.  Arecibo and Coamo had recently been founded.

Scarcely any progress in the settlement of the country was made during the remaining years of the seventeenth century.  Toward the middle of the eighteenth century great steps in this direction had been made.  From Governor Bravo de Rivera’s list of men fit for militia service, we discover that in 1759 there were 18 new settlements or towns in the island with a total of 4,559 men able to carry arms; exclusive of San Juan and San German, they were: