Good versus Evil
The most prominent theme in the parable of the pearl is that of the struggle between good and evil. As is the case with most parables the characters and events of the story are rendered more definitely aligned with good or evil than would be possible to appreciate amongst the degree of overlap inherent to the real world. Throughout the story the songs that Kino hears in his head reveals to him on an instinctual level of a person or thing's true nature. Thus, the song of evil accompanies the Priest who treats the indians like children and the doctor who regards them as animals. The song of the family, or the song of life, accompanies the life-sustaining morning activities as well as the family itself as they flee from their pursuers. In Kino's conception of good and evil anything that threatens the family is evil. Thus the song of evil can also accompany natural things like the scorpion which stings Coyotito. The pearl, also a product of nature, is never clearly defined as inherently good or evil. Rather its effect upon the family is shown to be evil once it has proven to be a treacherous repository of Kino's dreams.

Poverty versus Wealth
The pearl's immediate and lasting effect upon Kino is to cause him to dream of better things for himself and for his family. Although the pearl attracts attackers and pursuers, Kino is determined that it shall be the means by which his family rises above their station and, most importantly, his son achieves literacy. In this manner the story is a political one. The story delineates and draws moral conclusions about the differences between early nineteenth century Mexico's poor, characterized by the sympathetic characters such as Kino and Juana and the country's rich portrayed using unsympathetic characters like the doctor.

Family
Although Kino begins the story with the "song of the family" coursing through his being, he is soon sidetracked by the desires generated by the pearl. Though these desires are for things that Kino believes will make the family stronger - a rifle, a marriage, education - It is Juana who struggles to maintain the family as it once was. Significantly, it is Juana who first suggests destroying the peal between two stones and actually attempts to free her family of its influence by throwing it back into the sea. She realizes that the family would have no meaning without Kino and relents to his desire to sell the pearl in the city. Just as the family is what drives Kino's desires, so does the sense of family bind Juana to his side when she refuses to part with him during their flight into the mountains. Once Coyotito has been killed, however, the family has ceased to exist and Kino can see that the pearl, contrary to his initial belief, has brought nothing but bad fortune.

Fortune
The operations of chance and the effort to discern good luck from bad luck in an underlying theme in the story. The pearl itself is the byproduct of a chance grain of sand embedding in an oyster. Additionally, Kino's finding of the pearl is depicted as the lucky moment of collusion of being in the right place at the right time with the right need. The luck that that the pearl brings Kino's family, however, is revealed to be bad luck when his attempt to sell it at a fair price leads to the death of his only son.