Genealogy
Before Go-Mizunoo's accession to the Chrysanthemum Throne, his personal name (his imina) was Kotohito (政仁?) or Masahito.
He was the third son of Emperor Go-Yōzei. His mother was the daughter of Konoe Sakihisa.
Go-Mizunoo's Imperial family lived with him in the Dairi of the Heian Palace. The family included at least 33 children; and four of them would occupy the throne.
- Chūgo: Tokugawa Masako (daughter of Tokugawa Hidetada), later known as Tōfuku-mon'in.
- Imperial Prince Takahito (1621–1628)
- Imperial Princess Kazu-no-miya Okiko (女一宮興子内親王): became Empress Meishō
- Consort: Sono (Fujiwara) Mitsuko, Daughter of the Sadaijin (the Minister of the Left)
- Imperial Prince Suga-no-miya Tsuguhito (素鵞宮紹仁親王): became Emperor Go-Kōmyō
- Imperial Prince Morizumi (守澄法親王, Morizumi-shinnō?, 1634–1680): in 1654, becomes abbot of Kan'ei-ji in Ueno, known as Rinnōji no miya.
- Lady-in-waiting: Kushige (Fujiwara) Takako, Daughter of Sa Konoe Chūjō(左近衛中将,Vice-Secretary of left Imperial Guard).
- Imperial Prince Hide-no-miya Nagahito (秀宮良仁親王): became Emperor Go-Sai
- Imperial Prince Yasuhito (穏仁親王, Yasuhito-shinnō?, 1643–1665): later adopted into the Katsura no miya princely house.
- Lady-in-waiting: Sono (Fujiwara) Kuniko, Daughter of the Nadaijin (later known as the Lord Keeper of the Privy Seal)
- Imperial Prince Ate-no-miya Satohito (高貴宮識仁親王): became Emperor Reigen
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