The emigration of upper-class Dominicans served to forestall rebellion and to prolong the period of Haitian occupation because most Dominicans reflexively looked to the upper class for leadership. Scattered unrest and isolated confrontations between Haitians and Dominicans undoubtedly occurred; it was not until 1838, however, that any significant organized movement against Haitian domination began. Crucial to these stirrings was a twenty-year-old Dominican, of a prominent Santo Domingo family, who had returned home five years earlier after seven years of study in Europe. The young student's name was Juan Pablo Duarte.

Dominican history can in many ways be encompassed by a series of biographies. The personality and attributes of Duarte, however, ran counter to those of most of the country's caudillos. Duarte was an idealist, an ascetic, a genuine nationalist, a man of principle, and a romantic in a romantic age. Although he played no significant part in its rule, he is considered the father of his country. He certainly provided the inspiration and impetus for the achievement of independence from Haiti. Shocked, when he returned from Europe, by the deteriorated condition of Santo Domingo, the young student resolved to establish a resistance movement that would eventually throw off the Haitian yoke. He dubbed his movement La Trinitaria (The Trinity) because its original nine members had organized themselves into cells of three; the cells went on to recruit as separate organizations, maintaining strict secrecy, with little or no direct contact among themselves in order to minimize the possibility of detection or betrayal to the Haitian authorities. Young recruits flocked to Duarte's banner (almost literally, for it was Duarte who designed the modern Dominican flag) as a result of the pent- up resentment under Haitian rule. Despite its elaborate codes and clandestine procedures, La Trinitaria was eventually betrayed to the Haitians. It survived largely intact, however, emerging under the new designation, La Filantrópica , to continue its work of anti-Haitian agitation.

Despite their numbers and their base of popular support, the Trinitarios (as the rebels still referred to themselves) required a political disruption in Haiti proper to boost their movement toward its ultimate success. The overthrow of Jean Pierre Boyer in the Revolution of 1843 provided a catalyst for the Dominican rebels. Charles Rivière-Hérard replaced Boyer as president of Haiti. Like most Haitian leaders, he required a transition period in which to deal with competitors and to solidify his rule. Rivière-Herard apparently identified one disaffected Haitian faction in the administration of the eastern territory; his crackdown on this group extended to the Trinitarios as well, because apparently there had been some fruitless contacts between the Dominicans and some liberal Haitians. The increased pressure induced Duarte to leave the country temporarily in search of support in other Latin American states, mainly Colombia and Venezuela. In December 1843, a group of Duarte's followers urged him to return to Santo Domingo. They feared that their plans for an insurrection might be betrayed to the Haitians and had therefore resolved to carry them through quickly. Duarte sailed as far north from Caracas as the island of Curaçao, where he fell victim to a violent illness. When he had not arrived home by February 1844, the rebels, under the leadership of Francisco del Rosario Sánchez and Ramón Mella , agreed to launch their uprising without him.

On February 27, 1844--thereafter celebrated as Dominican Independence Day--the rebels seized the fortress overlooking the Ozama river in the capital. The Haitian garrison, taken by surprise and apparently betrayed by at least one of its sentries, retired in disarray. Within two days, all Haitian officials had left Santo Domingo. Mella headed the provisional governing junta of the new Dominican Republic. Duarte, finally recovered, returned to his country on March 14. The following day he entered the capital amidst great adulation and celebration. As is so often the case in such circumstances, the optimism generated by revolutionary triumph would eventually give way to the disillusion caused by the struggle for power.

Pedro Santana 's power base lay in the military forces mustered to defend the infant republic against Haitian retaliation. Duarte, briefly a member of the governing junta, for a time commanded an armed force as well. He was temperamentally unsuited to generalship, however, and the junta eventually replaced him with General José María Imbert . Duarte assumed the post of governor of the Cibao , the northern farming region administered from the city of Santiago de los Caballeros, commonly known as Santiago. In July 1844, Mella and a throng of other Duarte supporters in Santiago urged him to take the title of president of the republic. Duarte agreed to do so, but only if free elections could be arranged. Santana, who felt that only the protection of a great power could assure Dominican safety against the Haitian threat, did not share Duarte's enthusiasm for the electoral process. His forces took Santo Domingo on July 12, 1844, and they proclaimed Santana ruler of the Dominican Republic. Mella, who attempted to mediate a compromise government including both Duarte and Santana, found himself imprisoned by the new dictator. Duarte and Sánchez followed Mella into prison and subsequently into exile.

Although in 1844 a constituent assembly drafted a constitution, based on the Haitian and the United States models, which established separation of powers and legislative checks on the executive, Santana proceeded to emasculate the document that same year by demanding the inclusion of Article 210, which granted him untrammeled power "during the current war" against Haiti.

As it turned out, the Dominicans repelled the Haitian forces, on both land and sea, by December 1845. Santana's dictatorial powers, however, continued throughout his first term (1844-48). He consolidated his power by executing anti-Santana conspirators, by rewarding his close associates with lucrative positions in government, and by printing paper money to cover the expenses of a large standing army, a policy that severely devalued the new nation's currency. Throughout his term, Santana also continued to explore the possibility of an association with a foreign power. The governments of the United States, France, and Spain all declined the offer.