Begonia molleri is endemic to the 854 km2 (330 sq mi) São Tomé Island, part of Africa’s second least-populous nation (São Tomé and Príncipe). It is one of four species of Begonia endemic to São Tomé Island. An additional species is native to both islands, while three other species which occur on São Tomé Island can also be found on mainland Africa.
Evidence points to this species being a paleoendemic–it is believed to have once had a much broader range, prior to the Pleistocene (see: Plana, V. et al. 2004.