The Holy Genesis Era is the second known era, covering the events of Genesis of Aquarion. This era is actually an altered recreation of the Celestial Genesis Era.

In this world, Sirius de Alisia is still alive and Scorpius' name is removed from the Book of Holy Genesis. At the end of the series, the Earth is split into two; Altair and Vega; the ''dark" and "light" sides of Earth.