Begonia elnidoensis is an endemic species of Begonia discovered in El Nido, Palawan, Philippines. The species was compared to Begonia wadei, in that both species have thick-trunked stem, differing in the widely to very widely ovate or subtriangular leaves, with the latter having obliquely ovate leaves, 3-4 secondary leaf veins where the latter has 6 on each side of the midrib, with glabrous petioles compared to latter having puberulous to tomentose, an inflorescence measuring 20–40 cm in length compared to only 6–20 cm, and the differently-sized bracts and capsules.
The specific epithet elnidoensis derives from El Nido, Palawan where the species was first discovered.