His father was the 3rd of the Fushimi-no-miya line and grandson of the Northern Pretender Emperor Sukō, making Go-Hanazono the great-grandson of Sukō and 3rd cousin to his predecessor, Emperor Shōkō. He was also the great-great-great grandson of Emperor Go-Fushimi. This is the second most remote relationship between an emperor and his successor after that between Emperor Go-Komatsu (both the sixth Northern Pretender and the 100th in the main line) and his predecessor in the official line, Emperor Go-Kameyama, who was his fourth cousin twice removed.