Rafflesia produces the largest single flowers in the world, at the expense of its host vine, Tetrastigma, yet it begins as an inconspicuous endophyte. It is unknown how the Rafflesia seed gets into the host and germinates. Multiple locals claim to have successfully grown the holoparasitic flower from seeds resulting in blooms. Using available morpho-histological studies, combined with descriptions from local Rafflesia seed growers, as well as unpublished details of our own work, we filled in the missing details of Rafflesia’s life cycle from seed germination to endophyte inside the host before it transitions to its flowering stage. Post-germination, the Rafflesia endophyte forms a clonal network of vegetative meristematic cells, separated by the dividing host tissue, each meristematic cell cluster eventually developing into the primordial floral bud or protocorm. We propose future work involving mass spectrometry imaging to characterize the metabolites that allow communication between distant endophytic clusters and floral bud induction without destroying the histology of the sample.