Self-sacrifice
At the core of San Manuel Bueno, Martyr is the idea of self-sacrifice. The theme is present even in the title; a martyr refers to one who dies for a cause or ideology. Don Manuel, the saint of Valverde de Lucerna, certainly spends his life hard at work for his villagers, chopping firewood and helping the sick. However, this alone would not normally qualify him for the title of martyr. Rather, it is because Don Manuel does so at the cost of his own happiness and well-being that he earns this title.
Don Manuel's struggle to reconcile his conflicting personal beliefs—his atheism and his role as a priest—is so great that he describes his life as "a kind of continuous suicide, or a battle against suicide, which is the same thing." The fact that he persists in his duties regardless inspires Angela and Lazaro Carballino, who in turn sacrifice their ideals for the sake of their community.
Knowledge/Truth
The Carballino siblings are two of the most educated villagers in Valverde de Lucerna. Angela Carballino grew up reading her father's many books, and her brother Lazaro spent many years in the progressive cities of the New World. As such, the two are strong proponents of education and the search for the "capital-T Truth." However, when they learn of their priest Don Manuel's true beliefs about religion, they wrestle with the possibility that it might not always be best for the Truth to be brought to light.
Throughout the story, Angela constantly seeks to understand Don Manuel's relationship with the Truth; she asks him what he believes to be true, and wonders why he conceals his true beliefs from others. However, both Angela and Lazaro eventually adopt Don Manuel's philosophy, giving up Truth as the ultimate ideal and resigning themselves to telling white lies to their villagers. At the climax of the story, Lazaro undergoes a public religious ceremony in the village, announcing that he has finally converted to Catholicism—a proclamation that is, ultimately, a falsehood that undermines Truth in exchange for the happiness of the villagers.
Identity
The nivola addresses two contrasting forms of identity: personal identity and social identity. The main characters of the story—Angela, Lazaro, and Don Manuel—each suppress their personal, true identities and beliefs in order to uphold their public identities and responsibilities. As such, despite Lazaro's pronounced atheism, he tells his religious mother on her deathbed that he will pray for her every night; Lazaro believes that, as a son, it his his responsibility to ensure that his mother dies feeling contented rather than unfulfilled.
Life and Death
Though life and death traditionally represent opposites, San Manuel Bueno, Martyr suggests that the true relationship between the two may be trickier than it seems. The first complication comes through the form of religion: although it seems that death is the end of life, Catholicism teaches that death is actually a vehicle for entering heaven, an eternal afterlife. The second comes through Don Manuel's personal philosophy. Not only does he consider his own life to be a "continuous suicide," he also refers to life as a "continuous dream" and thinks of death as "an eternal sleep, a sleep without dreams."
The third and final complication comes through Lazaro Carballino's interpretation of death. When he dies, he says that "a piece of Don Manuel will die with him." However, he also says that "the rest of Don Manuel will continue to live through Angela, until even those who are dead will die completely." Through this, Lazaro implies that people experience two deaths: their physical death, and the death that comes when one's influence is forgotten forever. Lazaro's philosophy forces the reader to ponder what it means to die a second death, and consider if it is then possible for one to live forever.
Religion
The nivola grapples with the nature of religion, including its purpose and function within communities. At the beginning of the story, Angela believes that religion serves to educate people about the true nature of things. In contrast, Don Manuel quotes Karl Marx when he says, "religion is the opium of the people. So let's give them opium, so they can sleep, and so they can dream." Don Manuel believes that religion serves not to tell people the truth, but to blind them to them so that they may live a hope-filled and happy, if ultimately deluded, life.
