Citi said that Javier Arrigunaga was stepping down "in light of the difficult challenges our franchise in Mexico has faced over the past year."
In February Citi took a charge of about USD 235 million from profits, saying it discovered "significant" fraud on the books of oil contractor Oceanografia after having lent it USD 585 million through a Banamex unit.
After that Citi fired a dozen employees involved with Banamex, including four managing directors.
Arrigunaga is being replaced by Ernesto Torres Cantu, currently CEO of Grupo Banamex unit Banco Nacional de Mexico.