During a Q&A with Kotaku in 2015, it was noted that both Danganronpa: Trigger Happy Havoc and Danganronpa 2: Goodbye Despair had a female character that appeared to have been designed to be the player/main character's favorite, the former game having Kyoko Kirigiri and the latter game having Chiaki Nanami. When asked if this was intentional, series creator Kazutaka Kodaka stated:

The game uses mist overlays during the "Man's Nut" shower scene to cover up Mahiru and Hiyoko, but the base image is more revealing, including drawn nipples for Mahiru.

Many of the attacks Monokuma uses on Monomi throughout the game are references to many famous attacks/characters from classic Shonen Jump manga.

• In Chapter 2, Monokuma uses the "Pegasus Meteor Fist" technique from Saint Seiya.
• In Chapter 3, Monokuma's punch references Rohan Kishibe's stand, "Heaven's Door" from JoJo's Bizarre Adventure.
• In Chapter 4, Monokuma uses the "Nine Headed Dragon Flash" technique from Rurouni Kenshin.
• In Chapter 5, Monokuma uses rapid punches and shouts "ORA ORA ORA" referencing JoJo's Bizarre Adventure.