The bīja or seed syllable used to represent Ganapati-Shōten is gaḥ (Devanagari: गः; Japanese pronunciation: gyaku), written in Siddham script. It is usually written double (गःगः), symbolizing his dual form.

The mantra considered to be the standard in Japanese Buddhism, identified in Amoghavajra's Rite of the Dual-bodied Vinayaka as Vinayaka's "heart mantra" (心呪) Oṃ hrīḥ gaḥ huṃ svāhā ॐ ह्रीः गः हुं स्वाहा On kiri(ku) gyaku un sowaka おん きり（く） ぎゃく うん そわか he mantra is traditionally interpreted as Vinayaka's seed syllable flanked by those of Avalokiteshvara (.Bonji-hrīḥ.svg / ह्रीः, hrīḥ) and Amritakundalin (BonjiHum2.png / हुं, huṃ), the two figures who subjugated him.