In 1839, no sooner had he began to make a name for himself than he was arrested for his opposition to Argentina's conservative caudillo, Juan Manuel de Rosas.
Three years later, the siege of Montevideo by Rosas's ally Manuel Oribe led Mármol to flee yet again, this time to Rio de Janeiro.
After an exile that had lasted thirteen years, he was elected a senator and later a national deputy from the province of Buenos Aires.
By coincidence, his two most notable successors in the office of chief librarian, Paul Groussac and Jorge Luis Borges, also suffered from blindness in their old age.
In Uruguay in 1847 he published six of what would eventually be twelve cantos of El Peregrino ("The Pilgrim"), a long autobiographical poem set to the rhythm of his changing fortunes, which drew heavily from Byron's Childe Harold's Pilgrimage.