The mood of "Rappaccini's Daughter" is initially apprehensive and foreboding. The narrator's early descriptions of Giovanni's lodgings as "high and gloomy" create a sense of foreboding, which intensifies when the narrator refers to a member of the family that owns the mansion "[partaking] of the immortal agonies of [Dante's] Inferno." Rich descriptions of the bewitching sensory beauty of Beatrice and Rappaccini's garden also cultivate a mysterious and suspenseful mood as the reader waits for the dark realities of the garden to be revealed.
To that end, the sense of foreboding further escalates as Giovanni's entanglement with Beatrice deepens and he discovers the effects of his relationship with Beatrice on his own body. At the end of the story, the mood turns frantic and horrified, culminating in Baglioni’s final, perverse exclamation, which he pronounces in a "tone of triumph mixed with horror": "'Rappaccini! Rappaccini!" he yells, "'and this is the upshot of your experiment!'" This final exclamation ends the story on a thundering and unsettling note, leaving readers with a feeling of unease.