Ryōbu Shintō scriptures place particular weight on genealogies that allow Shinto kami and esoteric Buddhist deities to be read as part of a single, continuous sacred history. Central among these is the line that runs from the primordial kami Izanagi and Izanami through their divine offspring, especially Amaterasu Ōmikami. This imperial-Amaterasu lineage is not merely repeated but reinterpreted, with Amaterasu identified with Dainichi Nyorai (Mahāvairocana), so that the imperial house and its ancestral kami are situated within a Buddhist cosmological framework. In this way, the familiar Shinto mythic genealogy becomes a bridge into the mandalic universe of esoteric Buddhism.

Alongside these divine and imperial lines, Ryōbu Shintō texts also foreground the formal transmission lineages of esoteric Buddhism, particularly those associated with Shingon and its founder Kūkai (Kōbō Daishi). These lineages trace the flow of dharma from Mahāvairocana through a series of patriarchs down to Japanese masters, and they are presented as parallel to, and ultimately harmonious with, the genealogies of the kami. By setting the imperial and kami lines next to the esoteric Buddhist transmission, the texts suggest that both arise from the same ultimate source, even as they retain their distinct narrative forms.

A further layer is added through explicitly syncretic genealogies, in which kami are treated as manifestations or trace-bodies of buddhas and bodhisattvas. Here the honji–suijaku logic is at work: buddhas and bodhisattvas function as the original ground, while the kami appear as their local, historically embedded forms. Genealogies in this mode show how specific kami, such as Amaterasu, are linked to particular buddhas like Dainichi Nyorai, thereby creating a vertical line of descent from cosmic enlightenment to local cult. Through such intertwined lineages, Ryōbu Shintō scriptures articulate a world in which Shinto and esoteric Buddhism are not rival systems but mutually illuminating expressions of a single sacred continuity.