Hoya flagellata is native to Southeast Asia, specifically from the island of Borneo.
It grows in the wet tropical biome, typically found in lowland to hill forests, often climbing trees as an epiphyte (or occasionally a lithophyte on rocks). Its natural habitat is characterized by high humidity, warm temperatures, and dappled or filtered light under the forest canopy.
Hoya flagellata was formally described by Rudolf Schlechter (1872-1925), a renowned German botanist. He published its description in 1908 in "Repertorium Specierum Novarum Regni Vegetabilis" (Repert. Spec. Nov. Regni Veg. 4: 33).
The specific epithet "flagellata" is Latin for "whiplash-like" or "like a whip," referring to its characteristic long, slender, often bare, and searching stolons (runners).