During the absence of Columbus from the colony, Don Peter Margarite, whom he had left with the command of the troops, instead of employing them prudently to keep the natives in awe, as he had been directed by the admiral, quartered them among the towns in the Royal Plain, where they lived at free quarters, to the utter ruin of the Indians, one of them eating more in a day than would suffice an Indian for a month. They besides lived in a most disorderly manner, devoid of discipline, and gave infinite offence to the natives by their licentiousness. The council to which the admiral had confided the government in his absence, reproved Margarite for allowing his troops to live in this disorderly manner, and endeavoured to prevail upon him to march about the island, as he had been directed by the admiral: But he refused to submit to their authority; and being afraid of being punished for his misconduct, he and Friar Boyle, and some other malcontents of the same party, took the advantage of the ships which brought out Don Bartholomew Columbus, and returned with them to Spain. On purpose to justify their own misconduct, and the desertion of their duty, these men represented at the court of Spain that the admiral had falsely represented the state of the West Indies, which they alleged did not produce any gold.

After the departure of their commander, the soldiers threw off all remains of subordination, and dispersed themselves in small parties about the island, to the great offence and oppression of the natives, whom they plundered at their pleasure. While in this state of dispersion, Guatiguana, the cacique of a large town on the banks of the Great river, killed ten of the Christians who had taken up their quarters in his town, and sent privately to set fire to a house in which several of the sick soldiers were quartered. Six more of the Spaniards were put to death by the Indians in other parts of the island; and the Christians became universally hated for their oppressive conduct to the natives. Four of the principal caciques, named Guarionex, Caunabo, Behechico, and Higuanama, with all their allies and subjects, who were prodigiously numerous, entered into a confederacy to drive the Spaniards out of their country. Guacanagari alone, of all the native chiefs, who was cacique of the district named Marien, refused to join in this hostile confederacy, and remained friendly to the Spaniards, about an hundred of whom he hospitably entertained in his province, supplying their wants as well as he was able. Some days after the return of the admiral to Isabella, this friendly chief waited on him, expressing much concern for his indisposition, and the troubles that existed between the Spaniards and the natives, declaring that he had taken no part in the disaffection of the other caciques, but had always remained steadfast in his friendship for the Spaniards, for which reason all the other chiefs were incensed against him, particularly those of the Royal Plain, and others who were in arms. He even wept on calling to mind the massacre of the Spaniards in the Nativity, because he had not been able to defend them against his countrymen till the return of the admiral; and on learning that the admiral meant to take the field to reduce the insurgent caciques, Guacanagari offered to join him with all his subjects who were able to carry arms.

As Columbus was still unable to take the field in person, he sent out others to make war on Guatiguana, that the natives might not grow too bold by the delay of punishment for having put the Spaniards to death. A great number of the subjects of that cacique were accordingly slain, and many more made prisoners, who were sent into Spain; but the cacique made his escape. Caunabo was at that period the most powerful of all the native caciques, his province of Maguana being very populous. As it appeared somewhat difficult to reduce this chief by force, the admiral employed Alonzo de Ojeda to attempt making him a prisoner by stratagem.

The Indians at this time put a greater value on brass and other metals brought from Spain than they did on gold, believing that it came from heaven; and when the bell of the church of Isabella rang, to summon the Christians to prayers, they thought that it actually spoke, calling it turey, which in their language signifies heaven. The fame of this bell had spread over the island, and Caunabo had often expressed his desire of begging it from the admiral. Ojeda took advantage of this fondness of the Indians for polished metals, and went on horseback into the country of Caunabo, accompanied only by nine mounted Spaniards, under pretence of carrying him a valuable present from the admiral. On his arrival in the province of Maguana, which was sixty or seventy leagues from Isabella, the natives were amazed to see him and his attendants on horseback, believing the man and horse to be one animal. Some of them, by desire of Ojeda, informed Caunabo that certain Christians were come from the admiral, whom they named Guamiquini, bringing him a magnificent present of turey, at which he was exceedingly glad. On his introduction to the cacique, Ojeda and his men shewed him every mark of profound respect, and then gave him a sight of the intended present, which consisted of fetters and handcuffs so curiously polished as to resemble silver. Ojeda told him that the kings of Spain wore such ornaments, which came from heaven, and always appeared in them at arcitos or solemn dances: But he stated that it was necessary, before Caunabo could put on these splendid ornaments, that he should go along with the Christians and purify himself by bathing in the river Yaqui, about half a league from his residence, after which he should put on the turey or heavenly ornaments, and come back to his subjects on horseback dressed like the king of Spain. Caunabo was completely imposed upon by this shallow artifice, little imagining that ten Spaniards would attempt any thing against him in his own country; he accordingly was prevailed on to accompany Ojeda and his men to the river, attended only by a small number of his dependants. Having washed and purified himself, as desired, and being exceedingly anxious to fit on the ornaments, he allowed himself to be lifted on horseback behind Ojeda, when the fetters and handcuffs were put on, the Indian attendants keeping at some distance for fear of the horses, of which they were in great dread. Ojeda rode gently about with him for a short time, as if shewing the cacique in his solemn new ornaments to his servants; then suddenly galloped off accompanied by the Spaniards, and soon carried him out of sight of the astonished Indians. The Spaniards now drew their swords, and threatened to put the cacique to death if he attempted to escape. They then bound him fast with ropes to Ojeda, and making the best of their way to Isabella, delivered him a prisoner to the admiral, who kept him for some time in his house always fettered. When the admiral happened to come into the room where he was kept, Caunabo never shewed him any respect, but always did so to Ojeda; and being asked his reason for this, he said the admiral durst not go as Ojeda had done, to seize him in his own dominions. Sometime afterwards, the admiral sent Caunabo and other Indians into Spain; but the ship in which they were was cast away in a storm, and all on board were lost. About this time, finding the ships which had accompanied him in exploring the islands, and those others which remained at Isabella, so much injured by worms as to be unfit for service, he ordered that two new caravels should be built with all speed, that the colony might not be without shipping; and these were the first ships that were constructed in the New World.