The roots of the MahaSiddha Tradition emerged from the indigenous Tantric spirituality of ancient India. Historically it is said that the dynamic healer and spiritual leader first known as Shiva was the first teacher of Tantra. Though it is clear that Shiva was the original Yogi who wore the cremation ground ornaments, carried the damaru and practiced Tantra, there is much disagreement between traditions as to how elements of Indian Tantra came to be intermingled with Buddhism. It is clear that it did happen; Indian Tantra was a crucial factor in the development of Buddhist Tantra.

In a traditional story, Tantric Buddhism was born after the wild form of Shiva, called Rudra, passed through a stage where his ego became horribly ugly and inflated. He was behaving so awfully that the Primordial Wisdom Buddhas intervened. Out of compassion, they gave him a transmission of realization beyond "self," which freed him from egoism. From that moment, though Rudra appeared as he was before, he had now realized emptiness of self and the Tantras of Buddhism were manifest. The origins of the MahaSiddha Tradition can be traced back to these and other indigenous Indian realized beings who expressed non-dual spirituality in it's primitive form.