Many prominent Dominicans were in doubt as to whether the republic would be able to maintain a stable government and resist the incursions of the Haitians, and believed that the best course for the safety and prosperity of the country would be to seek the protection of a foreign power. These men, who came to be known as conservatives and who counted Santana among their number, began to spread their doctrines and were bitterly opposed by a different element, calling themselves liberals, among whom were Duarte, returned from exile, and the members of the central council of government. A number of prominent conservatives were obliged to go into hiding in order to escape imprisonment, and the central council of government appointed Duarte its representative in the north and ordered that General Francisco del Rosario Sanchez supersede Santana in command of the troops in the south. Duarte was proclaimed president of the republic by the people of the north, but Santana's soldiers refusing to recognize any other leader, marched on the capital, which they entered on July 12, 1844, and deposed the central council of government, declaring Santana chief of state with dictatorial powers. Thus the unhappy series of revolutions which have done such harm to the Dominican Republic was inaugurated within five months after the declaration of independence.

Santana organized a new central council of government and sent emissaries to the Cibao, or northern part of the republic, where he won over the army and the principal leaders. Duarte, Sanchez and others who had risked their lives and spent their fortunes in behalf of Dominican independence were arrested, imprisoned in irons in the ancient "Tower of Homage" of Santo Domingo and exiled as traitors to their country!

A constitutional convention was called, which met at San Cristobal and drafted the first constitution of the Republic, taking the constitution of the United States as a model. It was promulgated on November 6, 1844. In accordance with a provision of the constitution that the convention elect the president for the first two terms, General Santana was chosen, as was to be expected. General Pedro Santana, who thus became the first constitutional president, was a rough, uncouth and uneducated man, but possessed of keen perception and great personal bravery. He had a strong strain of negro and probably also of Indian blood. Born in Hincha, he had left his native town during the troubles of the early part of the century and settled in the province of Seibo, where he acquired an ascendency over the population that made him a kind of local demigod.

Conspiracies against Santana's government were immediately set on foot by the liberals, but were discovered and three ringleaders were executed on the first anniversary of the Republic's independence. In the spring of 1845 the first Congress met and proceeded to organize the government.

In the meantime a guerilla warfare had been going on with the Haitians along the border, and President Pierrot, who had overthrown Hérard, was preparing to invade the Dominican Republic. His two armies were at first successful and captured several border towns, but that which entered in the south was repulsed at Estrelleta, while that which invaded the north was defeated at Beler. A small Haitian fleet which set out to attack Puerto Plata blundered on a shoal where it was left high and dry and captured by the Dominicans.

Steps were now taken to secure the recognition of the republic by foreign powers. The government soon found itself in financial difficulties, as it was expensive to maintain the country in a state of defense against the Haitians, and an issue of paper money without sufficient guarantees made matters worse. Revolutionary mutterings were heard, and though a number of leaders were shot, the public discontent grew greater and more apparent. Santana comprehended the situation and determined to resign the presidency, which he did on August 4, 1848. The cabinet officers temporarily carried on the government and called an election, as a result of which General Manuel Jimenez, who had fought the Haitians and had been secretary of war under Santana, was declared president, entering upon office on September 8, 1848.

In his efforts to face the economic troubles of the government Jimenez disbanded part of the army and reduced military expenses. The moment was inopportune, for the implacable Haitians, who continued to consider Santo Domingo as Haitian territory in revolt, were preparing for another invasion. Soulouque, who had attained the presidency of the black republic, made a sudden incursion and marched victoriously as far as Azua. The Dominican government observed a vacillating policy which provoked general distrust and protests from the friends of Santana, whose partisans in the Congress called on him to take command of the army. Jimenez at first demurred but finally consented, and Santana, emerging from retirement, collected a few hundred ragged troops at Sabana Buey, near Azua. Soulouque attempted to move eastward by way of the canon of El Número, but was prevented by a Dominican force under General Duvergé; he then tried the pass of Las Carreras and was met and utterly defeated on April 21, 1849, by General Santana. The Haitians retreated to their own territory, burning Azua and other towns on the way. Quarrels between President Jimenez and Congress continued meanwhile, and his opponents induced the army to declare itself against the president and request General Santana "not to lay down his arms until a government was established which would respect the constitution and the laws and forever banish discord from Dominican soil." The Congress called the president to appear before it, and some of the officers of his staff, hearing him harshly criticised, drew swords and pistols to punish the offending congressman, and only the energy of the speaker, Buenaventura Baez, averted a bloody conflict. Congress adjourned to San Cristobal, the most important towns of the country rose against the administration, and Santana laid siege to the capital. After the siege had lasted a week, and the suburban town of San Carlos had been destroyed by fire, President Jimenez yielded to the arguments of the British, French and American consuls and agreed to resign the presidency and leave the country on a British warship. Santana entered the city at the head of his army on May 30, 1849, and assumed the reins of government, one of his first measures being a wholesale expulsion of Jimenez followers. He was crowned with honors by Congress and given the title of "Libertador."

The electoral college having been convened, Santiago Espaillat was chosen president, but refused to accept, realizing that Santana would expect to manage him as a puppet. Colonel Buenaventura Baez was then chosen and on December 24,1849, entered upon his first term as president of the Dominican Republic.

Baez, who was to play a leading part in the history of his country during the next thirty years, was the antithesis of Santana in manners and education. Born in Azua in 1812, the oldest of a family of seven children, his father had sent him to Europe to study and he returned one of the most polished and best educated Dominicans of his day. Under Haitian rule he was a member of the Haitian congress and of one of the Haitian constitutional assemblies. Almost white himself, he here distinguished himself by his boldness in opposing measures restricting the rights of whites in Haiti. After the declaration of independence of Santo Domingo he was a member of the first constitutional assembly and speaker of the first congress, being elected from the province of Azua, where his influence was similar to that enjoyed by Santana in Seibo. Until he became president he was a close friend of Santana.

Baez determined to take the offensive against Haiti, and a small naval campaign was undertaken in which Dominican government schooners captured Anse-à-Pitre and one or two other villages on the southern coast of Haiti, which were sacked and burned by the Dominicans. At the same time Baez requested the mediation of the United States, France and England to put an end to the struggle between Haiti and the Dominican Republic. Soulouque, who had meanwhile proclaimed himself Emperor of Haiti, offered to agree to peace and recognize Baez, but on condition that the Haitian flag be raised in Santo Domingo and the sovereignty of Haiti be admitted. His conditions were naturally rejected by the Dominicans, and the mediating powers informed the negro emperor that if he persisted in his plans of invading Santo Domingo they would be obliged to impose a suspension of hostilities for ten years. Nevertheless his forces continued to mass on the frontiers and small bodies actually entered Dominican territory, but were driven back. Upon the protests of the three powers Soulouque explained the incursions as having been due to disobedience to orders, and under pressure agreed to a truce for one year, during which negotiations were to continue for a definite treaty of peace or an armistice of ten years. In December, 1852, the minister of foreign affairs of France notified Haiti that the maritime nations of Europe were disposed to maintain the independence of Santo Domingo.