Don Juan Crisóstomo Eibarramendia y Magsalin, commonly referred to in the novel as Ibarra
or Crisóstomo, is the novel's protagonist. The mestizo (mixed-race) son of Filipino
businessman Don Rafael Ibarra, he studied in Europe for seven years. Ibarra is also María Clara's fiancé. María Clara de los Santos y Alba, commonly referred to as María Clara, María, or Clarita, is Ibarra's fiancée and the most beautiful and widely celebrated girl in San Diego. She was raised by Kapitán Tiago de los Santos, and his cousin, Isabel. In the later parts of the novel, she was revealed to be an illegitimate daughter of Father Dámaso, the former curate of the town, and Doña Pía Alba, Kapitán Tiago's wife, who had died giving birth to María Clara. Don Tiburcio de Espadaña – A Spanish quack doctor who is weak and submissive to his pretentious wife, Doña Victorina. Dámaso Verdolagas, better known as Padre Dámaso, is a Franciscan friar and the former parish curate of San Diego. He is notorious for his brashness and cruelty during his ministry in the town. An enemy of Crisóstomo's father Don Rafael Ibarra, Dámaso is revealed to be María Clara's biological father. Narcisa, or Sisa, is the deranged mother of Basilio and Crispín. Described as beautiful and young, she loves her children very much but cannot protect them from beatings by her husband, Pedro. Crispín is Sisa's seven-year-old son. An altar boy, he was unjustly accused of stealing money from the church. The head sexton beats him to force him to "return" the money. Basilio dreams that Crispín dies of the beating. Basilio is Sisa's 10-year-old son. An acolyte tasked with ringing the church's bells for the Angelus, he faced the dread of Crispín's death and his mother's descent into insanity. Elías asked him to cremate his and Sisa's body after revealing the location of Ibarra's treasure. Tíya Isabel – Kapitán Tiago's cousin, who helped raise María Clara and served as a surrogate mother figure. Don Santiago de los Santos, known by his nickname Tiyago and political title Kapitán Tiyago, is said to be the richest man in the region of Binondo and possessed real properties in Pampanga and Laguna de Baý. He is also said to be a good Catholic, a friend of the Spanish government and thus was considered a Spaniard by the colonial elite. Kapitán Tiyago never attended school, so he became the domestic helper of a Dominican friar who gave him an informal education. He later married Pía Alba from Santa Cruz. Padre Bernardo Salví – a Franciscan friar who succeeded Damaso as curate of San Diego. He lusts after María Clara. He is described to be very thin and sickly. It is also hinted that his surname, "Salví", is the shorter form of "salvación" ("salvation"), or that "Salví" is short for "salvaje" ("savage", "wild"), hinting at the fact that he is willing to kill an innocent child, Crispín, whom he accused of stealing money worth two onzas.
Padre Hernándo de la Sibyla – a short and fair-skinned Dominican friar. He is instructed by an
old priest in his order to observe and see Crisóstomo Ibarra's doings. Doña Victorina de los Reyes de de Espadaña, commonly known as Doña Victorina, is an ambitious Filipina who classifies herself as a Spaniard and mimics Spanish ladies by putting on heavy make-up. The novel narrates Doña Victorina's younger days: she had many admirers, but she spurned them all because none of them were Spaniards. Elías is Ibarra's mysterious friend and ally. Elías made his first appearance as a pilot during a picnic of Ibarra and María Clara and her friends.