The Cordillera Central is a vast mountain range, spanning 22,500 km² in the Philippines, containing some of the country’s last remaining intact forests. These forests are a reservoir for biodiversity and home to many poorly-known species, including those in the genus Rafflesia, renowned for containing the world’s largest flowers. Here we describe Rafflesia balatociana, a distinctive yet overlooked taxon from the high elevation moss forest, which we name after the Balatoc Indigenous Peoples, one of the subtribes in the Kalinga Province. This species is distinguished from its close relatives by a combination of conspicuous and stable characters including a double-dentate disk rim and strap-shaped lacuna on the annulus interior. We compare R. balatociana with co-occurring species in the Cordillera Central, provide a key, and consider our findings in the wider context of the exceptional biodiversity of this region and its conservation requirements. We propose R. balatociana should be classified as Critically Endangered, and recommend its habitat be declared as either a Critical Habitat Area (CHA) or a Local Conservation Area (LCA).