According to early drafts of the game, Lutz from the first Phantasy Star was originally going to be the main character. The plot involved him awakening from cryosleep 1000 years in the future with new powers and a different personality.

In the Japanese release of Phantasy Star II, the piano teacher, Ustvestia, is openly homosexual. When a male party member volunteers to be taught the Musik technique by Ustvestia, Ustvestia replies, "He looks cute." Ustvestia then proceeds to charge the male party member less for the lesson than he would charge a female party member.

However, in the English release of Phantasy Star II, Ustvestia simply says, "He looks smart." The gender-based disparity in the fee for learning Musik is left unexplained.