Work on the fortifications of the island was actively pursued during the administration of Gamboa. It was ordered that el Morro should have a garrison of two hundred, and that as soon as feasible, la Punta and la Fuerza were to be garrisoned by one hundred men each. The construction of the fort at the entrance to the port of Santiago de Cuba was an important improvement. It was called San Pedro de la Rocca, in honor of the governor of that city, D. Pedro de la Rocca, although it is generally known as the Morro. A garrison was installed, consisting of one hundred and fifty men sent from the Peninsula, and the ammunition destined for the defense came from New Spain. The power of the armadilla, which had theretofore been arbitrary, was also regulated at this time. Governor Gamboa, however, retired from office on the fifteenth of September, 1639, when he had barely inaugurated these improvements, and sailed for Spain.
Gamboa's successor was D. Alvaro de Luna y Sarmiento, a knight of the Order of Alcantara. During his administration, which began on the fifteenth of September, 1639, and ended on the twenty-ninth of September, 1647, the work of constructing defenses was eagerly pushed. Two leagues leeward of Chorrera a fort was erected. At the mouths of the rivers Casiguagas and Cojimar were built the two towers that had been planned by Governor Viamonte; they were intended to protect those advanced points of the capital. The able engineer Bautista Antonelli superintended the construction of these works of fortification. As the cost of these structures was defrayed by the inhabitants of the city, the governor saw fit to entrust their defense to three companies of men recruited from the native population. It was the first regiment of the kind organized on the island. By January of the next year the fortifications of the Castillo del Morro were also completed.
With the insurrection of Portugal which occurred at this period the pirates became bolder and renewed their outrages. The Dutch, too, threatened Havana once more. A squadron commanded by Admiral Fels had approached close to the coast, but had been driven back by a violent hurricane. Four of the vessels had been left between Havana and Mariel. Governor Luna sent Major Lucas de Caravajal against them; three hundred Dutch were taken prisoners, and seventeen bronze cannon, forty-eight iron cannons, two pedreros (swivel guns) and a great stock of arms and ammunition were captured. The captured pieces served to reenforce the artillery of the forts of La Punta and Morro.
D. Diego de Villalba y Toledo, Knight of the Order of Alcantara, became the successor of Governor Luna on the twenty-eighth of September, 1647. His assistant deputy was the Licentiate Francisco de Molina. A great calamity befell the island in the second year of his administration. A terrible epidemic broke out in the spring of 1649; the documents and chronicles of the period give hardly any details about the origin and the character of the disease, but it was most likely a putrid fever imported from the Indian population of Mexico and Cartagena by barges that had come from those places. The people who were attacked by it succumbed within three days, and it was estimated that in the course of five months one third of the population died.
Among those who died as victims of the scourge were the deputy auditor Molino and the three licentiates who succeeded him, Pedroso, Torar and Olivares, an Alcalde and many other functionaries, one third of the garrison and a great number of the passengers and crew of the fleet which its general, D. Juan Pujedas, had held ready to station in Havana. Governor Villalba himself was seriously ill and only saved by utmost care. The ravages of the epidemic seriously disturbed not only the ordinary activities of the population, but also the regular routine of the administration.
During this period of suffering and sorrow the conduct of the religious orders of both sexes was so admirable as to deserve special mention and warm recognition. The monks and nuns received the sick in their monasteries and convents, tenderly cared for them and when they did not succeed to nurse them back to health, escorted the victims to their graves. Among those who individually distinguished themselves by this true Christian spirit was Padre Antonio de Jesus. After the epidemic had spent itself and Governor Villalba had recovered, he organized a company of militia lancers under the command of Martin Calvido la Puerta, one of the wealthiest men of Havana. Like many other governors of Cuba, Villalba became at the end the victim of calumny and cabal. The government of Spain relieved him from his office and the Oidor of Santo Domingo, D. Francisco Pantoja de Ayala, was charged with an investigation of the complaints and accusations brought against him.
The victories of the Dutch fleets in India, Brazil and Peru and their conquest of some of the West Indian Islands, as also England's expansion of her dominions and the growth of her naval power were cause for grave anxiety. Measures of defense and protection became the subject of interminable discussions in the official circles of Madrid and Havana. The governors sent over by the court were urged to multiply their effort to fortify Cuba and insure safety from attacks by covetous enemies. D. Francisco Gelder, Field-marshal and Knight of Calatravas, succeeded Villalba and was inaugurated on the twenty-eighth of March, 1653. One of his first official acts was to sever communication with Santiago and Bayamo, for these two towns were at that time ravaged by the same epidemic from which Havana had suffered. His preventative measure set an example which was soon after followed by the authorities of Trinidad, Sancti Spiritus, Puerto Principe, Baracoa and Remedios, and the spreading of the epidemic being checked, the island soon returned to normal conditions.
Like other governors before him, Gelder showed a deplorable leniency towards those elements of the population that carried on contraband traffic with negroes. But he displayed great energy in the persecution of pirates. During his administration Captain Rojas de Figuerosa captured the island of Tortuga, which had been a formidable base of corsair operations. The news of this exploit caused great rejoicing in Havana and was celebrated by a Te Deum under the direction of Bishop Torre. Gelder also devised a plan to protect Havana from invasion by land. He proposed to open a canal from the extreme interior bay running north and extending to the sea, which would have surrounded the town by water and make it practically safe. But the suggestion did not seem to meet with approval. Before any other plans could be drafted, he died of apoplexy, on the twenty-third of June, 1654, and in the interval between his death and the arrival of his successor from Spain, the government was administered by the Regidor D. Ambrosio de Soto and D. Pedro Garcia Montanes, commandant of Morro.
The newly appointed governor, Field-marshal D. Juan Montano Velasquez, was inaugurated in June, 1655, but dying within a year, did not vitally influence the course of affairs in the island. His plan of fortifying Havana consisted in enclosing the city with walls from the landside, running a rampart with ten bastions and two half-bastions. For the execution of this plan the neighborhood of Havana offered to contribute nine thousand peons (day-laborers) and the town corporation imposed a tax on every pint of wine sold to assist in defraying the expenses of the construction. The king approved heartily of these offers and ordered that the treasury of Mexico should aid by an additional contribution of twenty-thousand pesos. But the historian Arrato reports that the whole scheme was soon after abandoned on account of the war in which Spain was about to be involved.
The British, their appetite for colonial possessions once being awakened, saw in the growing weakness of Spain an opportunity to get hold of some of her dominions. It was well known that Cromwell, although England was then at peace with Spain, tried hard to increase and strengthen its political and commercial power in America. The British had already conquered the islands Barbadoes and San Cristobal, and in the year 1655 a squadron of fifty-six vessels and a great number of transports sailed from England, determined to wrest from Spain more of her West Indian possessions. A force of nine thousand men was on these vessels, many of them filibusters who had joined the British.