One of the novel's main conflicts is Simoun seeking revenge against the Spanish colonial government and the wealthy Filipinos who have become corrupt and indifferent to the plight of the poor.
Juanito Palaez and Isagani’s rivalry for the love of Paulita Gomez.
Simoun’s revenge against the friars, particularly, Padre Salvi, who destroyed his reputation and possibly killed and r*** his fiancé inside the convent, Maria Clara.
Religious Hypocrisy when there is a conflict between genuine faith and religious hypocrisy by the corrupt clergy.
Cultural Identity and Nationalism Crisis is also very evident as Filipinos in the story succumb to foreign influences.