The return of Antonio de Torres into Spain with the twelve ships gave much pleasure to their Catholic majesties, who signified to the admiral by his brother Don Bartholomew their entire satisfaction with his conduct, giving him many thanks for all his toils and dangers in their service, expressing much concern for the affronts which had been offered to his person and authority, and promising always to support him in the exercise of his government. They ordered him to send home Bernal de Pisa in the next ships, and to appoint such person as he and Friar Boyle thought proper, in his place of head alguazil. To satisfy the admiral, and to promote the prosperity of the new colony, they ordered Rodriquez de Fonseca immediately to fit out four ships with such articles as the admiral desired might be sent to him, and appointed Antonio de Torres to return with these to the West Indies. He brought letters from their majesties to Columbus, dated at Segovia the 16th of August, in which they thanked him for his exertions in their service, promising to shew him all manner of favour, seeing that he had performed all he had undertaken, as exactly as if he had known the land which he went to discover. They acknowledged the receipt of his letters, giving an account of his second voyage; yet wished him to be more particular in mentioning how many islands he had discovered; what names they were known by to the natives, and what new names he had given them; their distances from each other, and their productions; and an account of the nature of the seasons during the different months. Having sent him all those things which he desired for the advancement of the infant colony, they requested him to send them all the falcons he could meet with, and other kinds of birds. Their majesties approved of all that he had done hitherto in regard to the government of the colony, directing him to continue in the same manner, giving every encouragement and countenance to those who conducted themselves properly, and discouraging all disorderly persons. They were quite satisfied in respect to the town he had founded, since he who was on the spot was necessarily the best judge, and they would have taken his advice if they had been themselves present. They gave him to understand that the controversy with Portugal was adjusted, sending him a copy of the articles of agreement; and as the settlement of the geographical line of partition was a matter of much importance and considerable difficulty, their majesties wished the admiral might be present along with the commissioners of the two crowns at fixing this boundary; but, in case he could not come himself, desired him to send his brother Don Bartholomew, or some other able persons, furnished with proper instructions and draughts for the purpose. And they requested this might be done as soon as possible, not to disappoint the king of Portugal. Finally, in order to receive frequent intelligence from him, they thought it advisable that a caravel should sail every month from Spain to the West Indies, and another return from thence to Spain.

The imprisonment of Caunabo gave great alarm, and infinite offence to his three brothers, who were all valiant men, and who now resolved to carry on war with all the energy in in their power against the Spaniards. Learning that all the country was in arms and collecting to an appointed rendezvous, the admiral, instead of waiting to be besieged in Isabella, determined to meet the Indians in the field. So many of his men were sick at this time, that he could only muster 200 foot and 20 horse. Yet with this small force, he marched from Isabella on the 24th of March 1495, accompanied by his brother Don Bartholomew, the adelantado or lieutenant-governor. Guacanagari, likewise, the constant friend of the Spaniards, accompanied him with all his forces; and part of the force employed by Columbus on this occasion, consisted of 20 blood-hounds, which made great havock among the naked Indians. Columbus marched to the Royal plain, where they found the Indian army drawn up under the command of Manicatex, appearing to amount to 100,000 men. Don Barthlomew gave the first charge, and the Spaniards acted with such vigour, assisted by their dogs, that the Indians were soon put to the rout with prodigious loss, great numbers being slain, and many made prisoners, who were made slaves of, a considerable number of them being sent to Spain in the four ships commanded by Antonio de Torres.

After this great victory, the admiral ranged for nine or ten months about the island, punishing such as he found most active in the revolt. For some time he met with considerable opposition from the brothers of Caunabo; but finding themselves unable to resist, they and Guarionex, being the most powerful caciques in the island, submitted at length to the admiral. On the complete reduction of the island, Columbus imposed the following tribute upon its native inhabitants. All the inhabitants from 14 years of age and upwards of the Royal Plain, the province of Cibao, and of other districts near the mines, were ordered to pay the fill of a small hawks-bell of gold dust every three months. Those of the other provinces were rated at a quarter of an hundred weight of cotton. The cacique Manicatex, who had headed the great insurrection, was condemned to pay monthly half a gourd, or calabash full of gold, which was worth 150 pieces of eight. To ascertain the regular payment of this tribute, certain medals of brass or copper were coined, every time the tribute fell due, and every tributary Indian received one of these to wear about his neck, that it might be known who had paid. Guarionex, the principal cacique of the Royal Plain, represented to the admiral that his subjects knew not how to gather the gold which was exacted from them, and offered to cultivate corn for the Spaniards all across the island, from the town of Isabella to where St Domingo was afterwards built, provided he would demand no gold from him. The distance between these two places is 55 leagues138, and the grain produce of this vast territory would have sufficed to maintain the whole population of Castile. The admiral was conscious that he was obnoxious to the ministers of their Catholic majesties, being an unprotected stranger, and that he could not support his interest in Spain, except by the transmission of treasure, which made him eager to procure gold from the natives: But the pressure of this tribute was so intolerable upon the Indians, that many of them abandoned their habitations and roamed about the island, to avoid the tax which they were unable to pay, seeking a precarious subsistence in the woods. In the sequel, finding this tribute could not be paid, its amount was lessened by the admiral.

The Indians had flattered themselves that the visit of the Spaniards to their country was only temporary, and used often to ask them when they meant to return home: But finding that they built stone houses, that they were much greater eaters than themselves, and were even obliged to bring part of their provisions out of Spain, many of the towns endeavoured to contrive to starve the Spaniards, so that they should either perish for want of food, or be compelled to return into Spain. For this purpose they discontinued the cultivation of provisions, and withdrew into the woods and mountains, trusting to wild roots and the vast numbers of an animal like a rabbit, called utias, for their subsistence. Although by this contrivance the Spaniards suffered greatly from want, and by ranging after the Indians, were often forced to feed on filthy and unwholesome things so that many of them died; yet the calamity fell heavily on the Indians themselves, who wandered about with their families in the utmost distress, not daring to hunt or fish, or to seek provisions, and skulking on the damp grounds, along the rivers, or among the mountains. Owing to these hardships and the want of proper food, a violent distemper broke out among the natives which carried off vast multitudes; insomuch that, through that illness and the casualities of the war, a third part of the population of the island had died by the year 1496.