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Background    Begonia  is a mega-diverse genus of flowering plants prone to generating micro-endemic species, especially on limestone habitats. During fieldwork in the Puerto Princesa Subterranean River National Park, Palawan (Philippines), three species were encountered which did not match any previously described from the region.    Results  Following morphological, anatomical, molecular phylogenetic and cytological investigation a hypothesis of three new species is supported. The three new species belong to a clade endemic to Palawan and Borneo.    Conclusions  The limestone habitats in the Puerto Princesa Subterranean River National Park environs support a unique flora. The description of three new species from a small area within the park demonstrates how much remains to be discovered there, and the importance of its continued protection.    Electronic supplementary material  The online version of this article (doi:10.1186/s40529-015-0099-1) contains supplementary material, which is available to authorized users.

Three new species of Begonia endemic to the Puerto Princesa Subterranean River National Park, Palawan