A huge theme of Bless Me, Ultima is understanding and questioning the dogma of organized faith. Antonio is already beginning to doubt the teachings of Catholicism when he first discovers the golden carp. Supposedly, its purpose is to guide the rest of the carp, who are the souls of sinners in a previous life. Antonio feels astounded that the carp is actually tangible and visible, and he gets a sense of enlightenment and religious fulfillment that he has never felt from Christianity.

The golden carp serves as an iconic symbol for Antonio's religious transformation. He even tries to show it to his agnostic friend, Florence, so that the latter might believe in something. However, Florence drowns before he can see the carp. This, combined with the carp's meaning to drown sinners, sets Antonio on a path of doubt once again.

Seeing the Golden Carp makes Antonio question everything he has been taught by his mother about the Catholic religion. He already has so many questions about life, such as why bad things happen to good people and why bad people aren't punished. After seeing the Golden Carp, his Christian God isn't able to cure his Uncle Lucas, but Ultima is able to save him. The priest had refused to help. Antonio is confused and wonders whether the Christian God cares. Later, Antonio decides Florence, his friend who doesn't believe in God, should see the Golden Carp because maybe Florence could believe in the latter. Florence dies before Antonio and Cico get the chance to show him.

The Golden Carp forces Tony to question his mother's Christian God.