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Bonifacio was born in Tondo, Manila. Her father was Santiago Bonifacio of Taguig, a tailor who served as a teniente mayor of Tondo, Manila. Her mother was Catalina de Castro, a native of Cabangan, Zambales, a mestiza born of a Spanish father and a Filipino-Chinese mother who was a supervisor at a cigarette factory. She was the fourth of six children. Her siblings were Andrés, Ciriaco, Procopio, Troadio and Maxima.