Bonifacio was the son of Santiago Bonifacio and Catalina de Castro in Tondo,Manila, and was the eldest of five children. His siblings were Ciriaco, Procopio, Troadio, Esperidiona and Maxima. His father was a tailor who served as a tenyente mayor of Tondo, Manila, while his mother was a mestiza born of a Spanish father and a Filipino-Chinese mother who worked at a cigarette factory.
Not finishing his normal education, Bonifacio was self-educated. He read books about the Revolution, biographies of the Presidents of United States, books about contemporary Philippine penal and civil codes, and novels . Aside from Tagalog and Spanish he could speak a little English, which he learned while working at J.M. Fleming and Co. Bonifacio was married twice: first to a certain Monica who died of leprosy then he married Gregoria de Jesus of Caloocan in 1893. They had one son named Andrés who died of smallpox in infancy.
In 1892 he joined Rizal's La Liga Filipina, an organization which called for political reforms in Spain`s colonial government of the Philippines. However, La Liga disbanded after only one meeting as Rizal was arrested and deported to Dapitan in Mindanao. Bonifacio, Apilinario Mabini and others revived La Liga in Rizal's absence and Bonifacio was active at organising local chapters in Manila. La Liga Filipina contributed moral and financial support to the Propaganda Movement of Filipino reformists in Spain. On 7 July