Simoun - Crisostomo Ibarra in disguise, left for dead at the end of Noli Me Tangere, has resurfaced as the wealthy jeweler, Simoun, sporting a beard, blue-tinted glasses, and a revolver. Fueled by his mistreatment at the hands of the Spaniards and his fury at Maria Clara's fate, he has since shed his pacifist image and become the titular "filibustero", pretending to side with the upper class and encouraging them to enslave the masses, while in reality siding with the masses and urging them to revolt against the oppressive Spanish regime. This time, he does not attempt to fight the authorities with knowledge, but by force. He concocts a plot to set off a bomb disguised as a beautiful lamp at a wedding where important members of civil society and the church hierarchy are in attendance. Unfortunately for him, his plan fails and he commits suicide by taking poison.
Basilio - Son of Sisa. A graduating Medical Student who befriended Simoun. This is the same Basilio introduced in Noli Me Tangere.
Isagani Villamor - Basilio's friend, ex-beau of Paulita Gomez and the man who removed the explosive lamp from the Captain Tiago's house, thus sabotaging Simoun's plans.
Kabesang Tales - Cabeza Telesforo Juan de Dios, a former cabeza de barangay (barangay head) of Sagpang, a barangay in San Diego's neighboring town Tiani, who resurfaced as the feared Luzón bandit Matanglawin
Don Custodio - Custodio de Salazar y Sánchez de Monteredondo, a famous "journalist" who was asked by the students about his decision for the Academia de Castellano. In reality, he is quite an ordinary fellow who married a rich woman in order to be a member of Manila's high society.
Paulita Gomez - The girlfriend of Isagani and the niece of Doña Victorina, the old Indio who passes herself off as a Peninsular, who is the wife of the quack doctor Tiburcio de Espadaña. In the end, she and Juanito Peláez are wed, and she dumps Isagani, believing that she will have no future if she marries him.
Macaraig - One of Isagani's classmates at the University of Santo Tomas. He is a rich student and serves as the leader of the students yearning to build the Academia de Castellano.
Father Florentino - Isagani's godfather, and a secular priest; was engaged to be married, but chose to be a priest after being pressured by his mother, the story hinting at the ambivalence of his decision as he chooses an assignment to a remote place, living in solitude near the sea.
Juli San Jose - Juliana de Dios, the girlfriend of Basilio, and the youngest daughter of Kabesang Tales. To claim her father from the bandits, she had to work as a maid under the supervision of Hermana Penchang. Eventually, she was freed but committed suicide after Father Camorra attempted to rape her.
Juanito Pelaez - A favorite student of the professors. They belong to the noble Spanish ancestry.
Doña Victorina - Victorina delos Reyes de Espadaña, known in Noli Me Tangere as Tiburcio de Espadaña's cruel wife. She is the aunt of Paulita Gomez, and favors Juanito Pelaez than Isagani. Although of Indio ideology, she considers herself as one of the Peninsular.
Father Camorra - The lustful parish priest of Tiani, San Diego's adjacent town who has longtime desires for young women. He nearly raped Juli causing the latter to commit suicide.