The haustorium in parasitic plants is an organ specialized for invasion and nutrient uptake from host plant tissues. Despite its importance, the developmental processes of haustoria are mostly unknown. To understand the dynamics of cell fate change and cellular lineage during the haustorium development, we performed live imaging-based marker expression analysis and cell-lineage tracing during haustorium formation in the model facultative root parasite Phtheirospermum japonicum. Our live-imaging analysis revealed that haustorium formation was associated with induction of simultaneous cell division in multiple cellular layers such as epidermis, cortex, and endodermis. In addition, we found that procambium-like cells, monitored by cell type-specific markers, emerged within the central region of the haustorium prior to xylem connection to the host plant. Our clonal analysis of cell lineages showed that cells in multiple cellular layers differentiated into procambium-like cells, while epidermal cells eventually transitioned into specialized cells interfacing with the host plant. Thus, our data provide the cell fate transition map during de novo haustorium organogenesis in parasitic plants.