The first president of Ecuador was not Ecuadorian. General Juan José Flores was Venezuelan, born in humble circumstances and raised on the battlefields of independence under Bolívar himself. When Gran Colombia collapsed, Flores was already governing Ecuador. He simply kept doing so, marrying into the criollo elite of Quito to cement his legitimacy. The new nation's treasury, however, emptied quickly. Military expenditures from the wars of liberation, along with a failed 1832 campaign to seize Cauca from Colombia, drained whatever revenue the fledgling state could raise. In 1833, four intellectuals publishing a newspaper called El Quiteño Libre dared to call the situation what it was: foreigners pillaging the national treasury. Authorities killed them. Flores was out of town, but the stain would not wash off.

When opposition forced a power-sharing arrangement in 1834, Flores pulled a maneuver worthy of Machiavelli. He embraced his rival, José Vicente Rocafuerte, sponsoring the Guayaquileno aristocrat for the presidency while retaining command of the army. For four years the two men alternated control. Rocafuerte, who had once condemned Flores's abuses, now justified his own iron hand with the argument that "the backwardness of Ecuador makes enlightened despotism necessary." He did build the country's first public school system. But when his term ended in 1839, Flores returned for a second presidency, then summoned a constitutional convention that rewrote the rules to keep him in power for eight more years. Opponents named the new document the Charter of Slavery. In one failed attempt to remove Flores the old-fashioned way, a young student named Gabriel García Moreno tried to assassinate him. The student missed. He would be heard from again.

By 1845 the country had had enough. An insurrection erupted in Guayaquil on March 6, led by General António Elizalde and Lieutenant Colonel Fernándo Ayarza. The rebels seized the artillery barracks. Flores, cornered at his plantation La Elvira near Babahoyo, surrendered and agreed to void every law and decree he had signed. He pocketed 20,000 pesos for the property and sailed for Spain. The coalition that overthrew him took their name from the month of their victory: marcistas, the men of March. They were an improbable alliance of liberal intellectuals, conservative clergy, and Guayaquil businessmen, and they began fighting each other almost immediately. Flores made matters worse from exile. In 1846 he proposed that a seven-year-old Spanish prince, half-brother to Queen Isabella II, be installed as King of Ecuador, with a grand scheme to fold Peru and Bolivia into the same crown. Spain and Britain briefly nodded. Then the whole fantasy collapsed.

The most consequential marcista turned out to be General José María Urbina, who seized power in 1851 and dominated politics for the next decade. His liberalism was defined by what it dismantled. One week after his coup, Urbina freed Ecuador's enslaved population. Six years later, his friend and successor Francisco Robles ended three centuries of annual tribute payments demanded from Indigenous peoples. For generations, criollo elites had taxed Native communities simply for existing within a country that had taken their land. Urbina and Robles also expelled a group of Jesuit priests in 1852 and tilted economic policy toward Guayaquil merchants rather than Quito landowners. In doing so, they drew the lines of an Ecuadorian political war that would last more than a century: liberal Guayaquil against conservative Quito, coast against sierra, commerce against hacienda.

Ecuadorians still call 1859 the Terrible Year. President Robles tried to settle the old English debt, inherited from Gran Colombia, by handing over national territory. Outrage exploded into four simultaneous governments claiming authority over the country: a provisional junta in Quito under García Moreno, a breakaway regime in Cuenca, a federal government in Loja covering the southern provinces, and Guillermo Franco's faction in Guayaquil. Peru's President Ramón Castilla blockaded the coast and played every side against the others. On November 14, 1859, aboard the Peruvian warship Amazonas, Franco signed a treaty with Castilla that ceded large territories and nullified decades of Ecuadorian border claims. García Moreno, desperate, wrote secret letters offering Ecuador as a French protectorate. France never answered. But Franco's betrayal accomplished what nothing else could: it united the other three factions against him, and against Peru.

Between September 22 and 24, 1860, at the Battle of Guayaquil, forces loyal to the Provisional Government, led ironically by the aging Juan José Flores, defeated Franco. García Moreno rode into power and began the conservative era that would shape Ecuador for the rest of the nineteenth century. The student who had once tried to kill Flores now ruled the country Flores had founded. Thirty years earlier, Bolívar had said those who served the revolution had plowed the sea. Ecuador's first three decades seemed to prove the point. And yet, by 1860, a recognizable nation had survived. Slavery had ended. Indigenous tribute had ended. The coast and the sierra had found the shape of their rivalry. The republic was bruised, compromised, and whole.