Challenges in morphology come to bear when assigning specific names in foliose Bangiales. Recent studies suggest that the integration of molecular and phenotypic data is essential, particularly in setting species boundaries and revealing the true species diversity of a given area. In an attempt to further elucidate the diversity of foliose Bangiales in the Philippines, two new species, Pyropia lunae sp. nov. and Pyropia islae sp. nov. are described. Each species differs from other closely related taxa by a combination of morphological and anatomical characters, and nucleotide sequences. Phylogenetic reconstruction based on rbcL gene sequences supports the sister relationship of P. lunae and Pyropia acanthophora, whereas P. islae is recovered as a species allied to Pyropia tanegashimensis and Pyropia denticulata. These two previously undescribed species increase the number of confirmed Philippine Pyropia species to four. So far, P. lunae and P. islae are found only from the Batanes Islands while P. acanthophora and P. tanegashimensis are known to extend their native distributions across into the Indo-Pacific waters. Questions remain, however, with regard to the true species diversity of foliose Bangiales in the Philippines. A wider sampling effort and the application of molecular methods will make it possible to resolve the remaining gaps in the taxonomy of Philippine foliose Bangiales.