Within forty years after its discovery Santo Domingo had passed the zenith of its glory. The vast and wealthy countries discovered and conquered on the mainland of America absorbed the attention of colonists and of the government, and Santo Domingo quickly sank to a position of economic and political insignificance. So little importance was given the island by chroniclers during the ensuing two hundred and fifty years and so few are the records remaining, that not even the names of all the governors and the periods of their rule can be accurately determined. The colony barely existed, the monotony of its life was interrupted only by occasional attacks or menaces of attacks by pirates or other foes.

Every effort was made to prevent decay. Decrees were issued forbidding emigration or the recruiting of troops for expeditions of discovery, but they were evaded. Thus Louis Columbus, the grandson of the Discoverer and one of the most influential men of the colony, fitted out an expedition against Veragua. African slaves continued to be imported to take the place of the exterminated Indians, but as their importation was expensive the mines were abandoned and the number of sugar estates declined. For the greater part of the period from 1533 to 1556 the government was in the hands of an energetic man, Licentiate Alonso de Fuenmayor, Bishop of Santo Domingo and La Vega, and later first Archbishop of Santo Domingo. He pushed to a conclusion the work on the cathedral and other religious edifices then building, repaired the edifices belonging to the state and constructed the walls and bastions which still surround the city. He was able to ward off the attacks of corsairs, who multiplied in West Indian waters to such an extent that in 1561 the Spanish Government forbade vessels to travel to and from the new world except under convoy.

In 1564 the cities of Santiago de los Caballeros and Concepcion de la Vega were completely destroyed by an earthquake and the few remaining inhabitants reestablished the towns at short distances from the original sites. The entire intercourse of the colony with Spain was reduced to two or three caravels a year and the revenues sank so low that the salaries of state officials were paid and continued to be paid for over two hundred years, from the treasury of Mexico.

The year 1586 was marked by the capture of Santo Domingo City by the noted English navigator, Sir Francis Drake, during the celebrated cruise on which he took the strongest towns on the Spanish main. On the morning of January 11, 1586, the inhabitants of Santo Domingo City were thrown into consternation at seeing eighteen foreign vessels in the roadstead, in a line which stretched from Torrecilla Point to the slaughterhouse. To the joy of the people the fleet set sail for the west, but their joy was short lived, for the next morning messengers arrived with the news that the enemy had landed at the mouth of the Jaina River and was marching on the city. Preparations were made for defense, but terror gained the upper hand and soon the civil and religious authorities, the monks and nuns and the entire population were fleeing in confusion on foot, in carts and in canoes, leaving their belongings behind. Some one hundred and fifty men remained to dispute the passage of Lieutenant-General Carliell who appeared at the head of a thousand men. They were quickly dispersed by the invaders who entered the gates with little loss and proceeded to the plaza where they encamped. For twenty-five days Drake held the deserted city, carrying on negotiations meanwhile for its ransom. When these flagged he ordered the gradual destruction of the town and every morning for eleven days a number of buildings were burned and demolished, a work of some difficulty on account of the solidity of the houses. Not quite one-third of the city was so destroyed when the residents paid a ransom of 25,000 ducats, about $30,000, for the remainder. Drake thereupon embarked, carrying with him the bronze cannon of the fort and whatever of value he found in the churches and private houses. He also ordered the hanging of several friars, held by him as prisoners, in retaliation for the murder of a negro boy whom he had sent with a flag of truce.

Seventy years later Santo Domingo was again attacked by English forces, this time with the object of making a permanent landing. Oliver Cromwell after declaring war against Spain sent a fleet to the West Indies under the command of Admiral William Penn, having on board an army of 9000 men. The fleet appeared off Santo Domingo City on May 14, 1655, and a landing was effected in two bodies, the advance guard under Col. Buller going ashore at the mouth of the Jaina River while the main body under General Venables disembarked at Najayo, much further down the coast. Buller met with strong resistance at Fort San Geronimo and was forced to retire to Venables' intrenchments. The united English forces made several attempts to march on the capital, but fell into ambuscades and sustained heavy losses. Despairing of success, the fleet and army left the island on June 3 and proceeded to Jamaica, which they captured.

The rovers of the sea and the restrictive trade regulations imposed by the Spanish government, which limited trade with the new world to the single port of Seville in Spain, made development of the island's commerce impossible. The trade restrictions had the effect of encouraging a brisk contraband traffic with Dutch vessels on the north coast, to stop which the Spanish government adopted the incredible expedient of shutting up every port except Santo Domingo City and ordering the destruction of the north coast towns. Puerto Plata, Monte Cristi and two villages on the coast of what is now Haiti were thus destroyed in 1606 and the inhabitants transferred to towns almost in the center of the island, where they were far removed from temptation to smuggle. The measure temporarily stopped contraband trade on the north coast, but destroyed all legitimate trade in that region, transformed the coast into a desert and furnished an opportunity for the settlement of the buccaneers in the northwest.

The English, French and Dutch, in resisting Spain's claim to sole trading rights in the new world, authorized the fitting out of privateers that often degenerated into pirates. The bays and inlets of the coast of Santo Domingo became favorite resorts for such ships. The depot of the corsairs on the island of St. Christopher having been destroyed by the Spaniards in 1630, a number of refugees sought shelter on the island of Tortuga, on the northwest coast of Haiti. Some of them began to cultivate the soil, others took to hunting wild cattle on the mainland of Haiti, while others indulged in piracy. Tortuga soon became the busy headquarters of reckless freebooters of all nations, who here fitted out daring expeditions and returned to waste their gains in wild carousals. In 1638 the Spanish governor of Santo Domingo made a descent on the island and destroyed the settlement, but most of the buccaneers were absent at the time and the only result of the raid was to cause them to organize under the captaincy of an Englishman named Willis. French national pride asserted itself, however, and with the assistance of a French force from St. Christopher, the English inhabitants of Tortuga, who were in a minority, were persuaded to leave for Jamaica, and Tortuga thenceforth continued under French governors.

In 1648 the Spaniards of Santo Domingo made another fruitless attempt to expel the buccaneers; but in 1653 the Spanish governor, the Count of Peñalva, collected a force which caught the island unawares and was strong enough to overawe the inhabitants, who were permitted to leave, though abandoning all their property. The Spaniards left a garrison but the persistent Frenchmen returned and drove it out. In 1664 the French West India Company took possession, established a garrison, and appointed as governor an energetic man, D'Ogeron, under whom the country rapidly advanced in prosperity and commerce. With the idea of encouraging permanent settlement, D'Ogeron had women brought over from the slums of Paris and portioned out as wives to the rude colonists.

The rapidly increasing population caused settlements to be made on the Haitian mainland, and the city of Port-de-Paix was founded on a beautiful bay opposite Tortuga. The city flourished to such an extent and the advantages of settlement on the mainland were so superior that the settlers of Tortuga gradually left the smaller island and settled along the Haitian coast. Within twenty years Tortuga was practically deserted and it so continues to this day.

A better class of people now arrived from France. Families were brought in from Anjou and Brittany, and the French settlements continued to spread all the way down the western coast of the island, the French settlement at Samana being withdrawn. Slaves were imported from Africa, and in 1678 a rising took place among them, which was easily put down. In 1684 the French government formally sent out commissioners to provide for the regular government of the colony, and churches and courts of justice were established.