After an outbreak of cholera in 1837, which the clergy blamed on the "godless" Liberals, the Conservatives incited an Indian revolt. A mestizo rebel leader, Rafael Carrera, seized Guatemala City in 1838, whereupon most of the member states went their own ways. By April 1839, only El Salvador remained loyal. 

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Carrera, Rafael [b. Oct. 24, 1814, Guatemala City; d. April 4, 1865, Guatemala City ]
dictator of Guatemala and one of the most powerful figures of 19th-century Central America.

Carrera was born of white and Indian stock, had no formal education, and remained illiterate all his life. Nevertheless, with the support of the Indian peasantry, who revered him, and the lower clergy, who despised the anticlerical liberal government, he captured Guatemala City in 1838 and took power, which he exercised completely and ruthlessly until his death.

Carrera--deeply religious, a strong nationalist, and a political conservative--consolidated his rule in 1840 when he became dictator and took Guatemala out of the United Provinces of Central America, proclaiming it an independent republic. 

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By 1839, the end of Morazán's second term, most of the member states had deserted the federation. A Conservative-backed rebel army under Rafael Carrera defeated Morazán at Guatemala City in March 1840, and he went into exile.