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Colonial Santa Cruz and revolutionary war

Over the next 200 years, several tribes were either incorporated under Spanish control or defeated by force. The city also became an important staging point for Jesuit missions to Chiquitos and Moxos, leading to the conversion of thousands of Guaranies, Moxeños, Chiquitanos, Guarayos and Chiriguanos that eventually became part of the racially mixed population of the modern Santa Cruz, Beni, Pando and Tarija departments of Bolivia. Another important role the small town played in the region for the Spanish Empire was to contain the incursions of Portuguese Bandeirantes, many of which were repelled by the use of force over the years. The efforts for consolidating the borders of the Empire were not overlooked by the authorities in Lima, who granted the province a great degree of autonomy. The province was ruled by a Captain General based in Santa Cruz, and, in turn, the city government was administered by two mayors and a council of four people. Citizens of Santa Cruz were exempt from all imperial taxes and the mita system used in the rest of the Viceroyalty of Peru was not practiced. However, in spite of its strategic importance, the city did not grow much in colonial times. Most of the economic activity was centered in the mining centers of the west and the main source of income of the city was agriculture.

Animosity towards imperial authorities began at the turn of the 18th century when the new system of intendencias reached the new world. The seat of government was taken away from the city and moved to Cochabamba, and many of the powers delegated by the viceroyalty were now in the hands of appointees of the crown. Like in many parts of Spanish America at the time, angered by the reforms the criollos saw as a threat to their way of life, and taking advantage of the Peninsular War, the local population, led by Antonio Vicente Seonane, revolted on September 24, 1810, overthrowing the governor delegate. A junta of local commanders took control of the government in his place. The revolutionaries, as it was the case with most of the revolts in Spanish America, remained loyal to the King of Spain, while repudiating the colonial authorities until after the end of the Peninsular War.

By 1813 the city was once again under imperial control. At this time, by order of General Manuel Belgrano, the revolutionary armies of Argentina sent a small force led by Ignacio Warnes to "liberate" Santa Cruz. After his successful campaign, he assumed control of the government of the city. In a little over a year Warnes was able to gather tremendous support from the population, enlisting criollos, mestizos and natives to the revolutionary army, and allying with the revolutionary leader of Vallegrande, Alvarez de Arenales, to defeat a strong imperial force in the Battle of Florida. This victory proved to be a serious blow to Spanish forces in the region. Nevertheless, two years after the victory of Florida, imperial forces launched a new offensive in the province led by Francisco Javier Aguilera. This campaign ended with the defeat and death of Ignacio Warnes and his forces in the Battle of Pari. Triumphant, Aguilera marched into the city with orders to quell the insurrection and reinstate the Spanish governor. This proved to be a very difficult task, with several revolutionary leaders, such as Jose Manuel "Cañoto" Baca and Jose Manuel Mercado, rising up in the coming years from the city itself and elsewhere in the province. These new leaders fought colonial authorities for seven years until they finally deposed the last Spanish governor, Manuel Fernando Aramburu, in February 1825 after news of the defeat of the imperial armies in the west had reached the city.