The Vitex trifolia complex in the Philippines comprises economically important medicinal species, but its taxonomic status has become ambiguous due to numerous historical nomenclatural revisions. We assembled the complete chloroplast genomes of five species belonging to this species complex to provide additional evidence for their species delimitation. Based on a detailed analysis of specimens which combined molecular and morphological data, we propose reinstating V. elmeri Moldenke and delineating V. arvensis Gentallan, Sengun & M.B.Bartolome as a new endemic species belonging to this complex. The new species is a putative hybrid between V. bicolor Willd. and V. elmeri Moldenke. The specific epithet arvensis reflects its predominantly cultivated nature, both on a commercial scale and in home gardens, as a valued medicinal plant. We also provided a key to identify the five species belonging to the V. trifolia complex in the Philippines.