Hannibal features prominent queer-coded and explicitly lesbian relationships. The intense bond between Will Graham and Hannibal Lecter is central, depicted with profound psychological depth and agency. Alana Bloom and Margot Verger's relationship is a source of strength against external threats. The show treats these relationships with dignity and complexity, affirming their worth within its dark narrative without judgment based on identity.

The show features several characters, including Dr. Alan Bloom, Freddy Lounds, and Beverly Katz, who were established as male in Thomas Harris's source novels but are portrayed as female in the series.

Jack Crawford, canonically white in the source novels, is portrayed by a Black actor. Beverly Katz, also white in the source material, is portrayed by a Korean-American actress. These instances constitute race swaps.

The show frequently employs Christian iconography and themes (sin, damnation, sacrifice) but often twists them to underscore profound psychological darkness and amorality. Traditional Christian morality is depicted as largely ineffective or inverted in the face of the show's pervasive evil, with religious concepts often co-opted or perverted by characters like Hannibal Lecter.