In 1519 occurred the last uprising of what was left of the first inhabitants of the island. Saved almost miraculously from the massacre of Anacaona's followers in 1504, Henri, a native of Bahoruco, was taken to Santo Domingo and brought up in a convent of Dominican friars. Though he became a Christian, he was nevertheless a slave. Tired of all the ill treatment inflicted on him by his master, incensed by an attempt on his wife's honor, and being unable to obtain justice, he fled in 1519; accompanied only by a few Indian slaves who swore to die rather than endure again the humiliation of their former condition, he took refuge in the mountains of Bahoruco.
This new leader could read and write; and like some of his companions he understood the use of firearms. They could therefore successfully hold their own. The Spanish pride received blow after blow. Henri's victories encouraged all the Indians who could make their escape to flock to his camp.
The black slaves were not long in following the example of their companions in misfortune. They rebelled on the very plantation of Diego Columbus, governor of the island. They set fire to all the farms they found on their way and killed every European they met. But, being without a leader and having only a slight knowledge of the country, they met with rapid defeat. Yet many of them were fortunate enough to reach the Ocao Mountains, where there lived already some men of their race, known as maroons, who had freed themselves from slavery.

The Spaniards failed to subdue Henri either by force or by deceit. He firmly established his authority in the Bahoruco, and his followers became the terror of the colonists. It was now his turn to inflict humiliations on the conquerors; which he did for more than fourteen years. The frequent defeats met by the Spaniards decided Charles V, then King of Spain and Emperor of Germany, to send a special agent to Hispaniola: Barrio-Nuevo was entrusted with the mission of restoring peace. Bearing a letter from the Emperor to Don Henri, he had no trouble in persuading the caciqueto lay down his arms. Acting by the advice of Las Cases, who was called the "Protector of the Indians," Henri went to Santo Domingo. A solemn treaty of peace was made and ratified on both sides. Henri was allowed to reside in the village of Boya. Exempt from paying tribute, he was to be called "cacique of Haiti" and to keep under his command the Indians who were permitted to follow him. These, numbering about 4,000, the last scions of the aboriginal race, settled at Boya. They had at last recovered their liberty. Henceforth they would be able to lead a quiet life.

The treaty signed in 1533 with the cacique Henri had at last put an end to the hostilities between the Indians and Spaniards. For a while there was no bloodshed. The relative tranquility which ensued was not taken advantage of. Instead of thriving, the colony was on the wane. The incompetency or malversation of the various governors hastened the decline. The mines were emptied or deserted; no care was given to agriculture. In consequence, through idleness, debauchery and poverty the colonists were in a piteous condition. Everything was falling to ruin. The town of Santo Domingo alone, where was centred the luxury of the administrators, remained prosperous and assumed, the appearance of great splendor. But its magnificence was the cause of serious calamities. In 1586 the English admiral, Sir Francis Drake, charged by Queen Elizabeth to curb the Spanish arrogance, bombarded the town, took possession of it, and partly destroyed it by fire. After an occupation of a month he agreed to evacuate it in consideration of a ransom of £7,000.

The arrival of other Europeans in the West Indies was to become a source of continual worry to the Spaniards. From the beginning of the sixteenth century, attracted by the allurements of gain, the French had begun making incursions into the New World. Impressed by the various tales concerning the riches of Santo Domingo city, they little by little commenced the habit of calling the whole island Saint-Domingue. At first they had no idea of conquest. They were satisfied with plundering. In concert with the English they lost no opportunity of injuring the Spanish trade. However, successive defeats made them feel the necessity of having a rallying-point, at least a place where they could refit their ships. In 1625 a party of Frenchmen under the command of Enembuc, and of Englishmen under the leadership of Warner, took possession of St. Christopher Island. Private initiative began thus to deprive Spain of its possessions in the West Indies.