A new variety of hornwort from northern Thailand, Phaeoceros perpusillus var. scabrellus is described based on morphological characters and molecular phylogenetic analyses. In this study, phylogenetic analyses supported that the new variety is closely related to P. perpusillus var. perpusillus. Morphologically, it is distinguished from the autonimic variety in nearly smooth spores under light microscope. A taxonomic description, illustrations, and light and scanning electron micrographs are provided. In addition, the new variety is assessed as Endangered (EN), demonstrating its rarity by being currently known from only three subpopulations.