The central conflict arises when a slave mother switches her infant son with her master's child, setting off a chain of events that exposes the moral decay and racial tensions of a small Missouri town. The protagonist, David 'Pudd'nhead' Wilson, serves as an outsider observer whose scientific curiosity and fingerprinting hobby eventually unravel the deception. He faces opposition from the rigid social hierarchy and the deep-seated prejudices of the community. The narrative framework utilizes a mix of dark irony and melodrama to critique the hypocrisy of the antebellum South.

Readers and critics frequently highlight the shift in Twain's tone toward a more somber and biting perspective in this work. Discussion often centers on the effectiveness of the fingerprinting plot as a precursor to modern detective fiction. Many observers note the balance between the sensationalist elements of the plot and the underlying social critique of racial inequality. The inclusion of the accompanying tales is often viewed as essential for understanding the breadth of Twain's late-career thematic concerns. Scholars frequently cite the work as a significant departure from his earlier, more lighthearted Mississippi narratives.