The incessant communications to the emperor, and even to the empress, on every subject more or less connected with the public service, but dictated mostly by considerations of self-interest, coming, as they did, from the smallest and poorest and least important of his Majesty's possessions, must have been a source of great annoyance to the imperial ministers, consequently they resolved to remove the cause. The Admiral was deprived of the prerogative of appointing governors, and henceforth the alcaldes (mayors) and "chief alguaciles" (high constables), to be elected from among the colonists by a body of eight aldermen (regidores), were to exercise the governmental functions for one year at a time, and could not be reelected till two years after the first nomination. The wisdom of this innovation was not generally acknowledged. The crown officers wrote: " … All are not agreed on the point whether the governor should or should not be elected among the residents of the island. For the country's good he should, no doubt, be a resident."
Alonzo la Fuente was of a different opinion. He wrote in November, 1536: "It has been a great boon to take the appointment of governors out of the Admiral's hands. As a rule, some neighbor or friend was made supreme judge, and he usually proceeded with but little regard for the island's welfare. All the rest were servants and employees of the Admiral, which caused me much uneasiness, seeing the results. Appoint a governor, but a man from abroad, not a resident." In the following year he wrote regarding the elective system just introduced: " … If the alcaldes must take cognizance of everything, this will become a place of confusion and disorder. A few will lord it over all the rest, and the alcaldes themselves will but be their creatures."
The new system of government was unsatisfactory. Castro and Castellanos asked for the appointment of a supreme judge in March, 1539, because an appeal to the authorities in la Española was made against every decision of the alcalde. Alderman La Fuente and Martel confirmed this in December, 1541. They wrote: " … There is great want of a supreme judge. More than fifteen homicides have been committed in less than eight years, and only one of the delinquents has been punished …" In January, 1542, the city officers sent a deputy to lay their grievances before the emperor, not daring to write them "for their lives," and in February the island's attorney, Alonzo Molina, stated the causes of the failure of the elective system to be the ignorance of the laws of those in authority and the reduced number of electors. "It is necessary," he said, "to name a mayor or governor who is a man of education and conscience, not a resident, because the judges have their 'compadres.'[35] The governor must be a man of whom they stand in fear, and if some one of this class is not sent soon, he will find few to govern, for the majority intend to abandon the island."
A law passed, it appears, at the petition of a single individual, in 1542, increased the confusion and discord still more. This law made the pastures of the island, as well as the woods and waters, public property. The woods and waters had been considered such from the beginning, but the pastures, included in the concessions of lands made at different times by the crown, were private property. The result of this law was aggression on the part of the landless and resistance on the part of the proprietors, with the consequent scenes of violence and civil strife.
Representations against the law were made by the ecclesiastical chapter, by the city attorney, and by the three crown officers in February, 1542; but the regidores, on the other hand, insisted on the compliance with the royal mandate, and reported that when the law was promulgated, all the possessors of cattle-ranges opposed it, and four of their body who voted for compliance with the law were threatened to be stoned to death and have their eyes pulled out. "We asked to have the circumstance testified to by a notary, and it was refused. We wanted to write to your Majesty, and to prevent any one conveying our letters, they bought the whole cargo of the only ship in port, and did the same with another ship that came in afterward…."
On the 2d of June following they wrote again: " … An alcalde, two aldermen, and ten or twelve wealthy cattle-owners wanted to kill us. We had to lock ourselves up in our houses…. The people here are so insubordinate that if your Majesty does not send some one to chastise them and protect his servants, there will soon be no island of San Juan."
The system of electing annual governors among the residents was abolished in 1544, and the crown resumed its prerogative with the appointment of Gerónimo Lebrón, of la Española, as governor for one year. He died fifteen days after his arrival, and the Audiencia named licentiate Cervantes de Loayza in his place, who was compelled to imprison some of the ringleaders in the party of opposition against the pasture laws. This governor wrote to the emperor in July, 1545: " … I came to this island with my wife and children to serve your Majesty, but I found it a prey to incredible violences…."
Cervantes was well received at first, and the city officials asked the emperor to prorogue his term of office, but as Bishop Bastidas said of the islanders, it was not in their nature to be long satisfied with any governor, and the next year they clamored for his "residencia." He rendered his accounts and came out without blame or censure.
It appears that about the year 1549 the system of electing alcaldes as governors was resumed, for in that year Bishop Bastidas thanks the emperor, and tells him "the alcaldes were sufficient, considering the small population." But in 1550 we again find a governor appointed by the crown for five years, a Doctor Louis Vallejo, from whose communications describing the conditions of the island we extract the following: "It is a pity to see how the island has been ruined by the attacks of Frenchmen and Caribs. The few people that remain in San German live in the worst possible places, in swamps surrounded by rough mountains, a league from the port…." And on the 4th of December, 1550: " … The island was in a languishing condition because the mines gave out, but now, with the sugar industry, it is comparatively prosperous. The people beg your Majesty's protection."
However, in October, 1553, we find Bishop Alonzo la Fuente and others addressing King Philip II, and telling him that "the land is in great distress, … traffic has ceased for fear of the corsairs…." The same complaints continue during 1554 and 1555. Then Vallejo is subjected to "residencia" by the new governor, Estevéz, who, after a few months' office, is "residentiated" in his turn by Caráza, who had been governor in 1547.