José de San Martín
Guayaquil conference

San Martín thought that if he joined forces with Bolívar he would be able to defeat the remnant royalist forces in Peru. Both liberators would meet in Quito, so San Martín appointed Torre Tagle to manage the government during his absence. Bolívar was unable to meet San Martín at the arranged date, so San Martín returned to Lima, but still left Tagle in government. Bolívar moved from Quito to Guayaquil, which secured its independence from Spain. There were discussions on the future of the region: some factions wanted to join Colombia, others to join Peru, and others to become a new nation. Bolívar ended the discussion by annexing Guayaquil into Colombia. There was Peruvian pressure on San Martín to do a similar thing, to annex Guayaquil to Peru.

The Guayaquil conference took place on 26 July 1822. They had two private meetings, on that day and the following one. As there were no witnesses or minutes, the content of their discussions can only be inferred from their later actions and their letters to other people. Some likely topics of discussion may have been a request of reinforcements, and an offer to combine the armies into a single one, with San Martín ranked second to Bolívar.

The minister Bernardo Monteagudo was removed from office by a Peruvian rebellion, during San Martín's absence. San Martín resigned as Protector of Peru a few days later and returned to Valparaíso, Chile. Several reasons influenced him to resign. The military discipline of the Army of the Andes was compromised, but San Martín was reluctant to take drastic action against his officers. The authority of San Martín and Bolívar, and the local rivalry of their respective countries Peru and Colombia, limited their options for joint work: Colombians would not have liked Bolívar to give many of his forces to San Martín, whilst Peruvians would not have liked their Protector to be second in command to Bolívar, and a joint command would complicate the maintenance of military discipline. Unlike Bolívar, backed up by the Colombian government, San Martín did not have more resources than those he already had: Buenos Aires denied him any support, the other Argentine governors (such as Juan Bautista Bustos) supported him but did not have resources to provide, O'Higgins was about to be deposed in Chile, and Cochrane took the navy and left him without naval power. Finally, he felt that only a very strong authority would be able to prevent balkanization, but refused to rule as a dictator himself.
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