Three species have been formerly segregated from Metzgeria in the genus Apometzgeria. One of the species, A. frontipilis, is endemic to South America but the second, A. pubescens, is currently understood as having a bipolar range with populations across the Holarctic and in southern South America. The third species, A. longifrondis, was described from China (and is not included in this study). Species of bryophytes that range across continents and have little or no morphological variation among populations may nevertheless harbor morphologically cryptic genetic lineages. We used nuclear and plastid sequence data to examine the phylogenetic relationship between Apometzgeria and Metzgeria, and phylogeographic patterns in taxa assigned to Apometzgeria. Two species often assigned to Apometzgeria are phylogenetically embedded within Metzgeria in two separate clades, one comprising all Holarctic A. pubescens and a second with A. pubescens from South America and all accessions of A. frontipilis. Phylogenetic and haplotype analyses reveal a lack of phylogeographic structure among A. pubescens plants from throughout its Holarctic distribution. However, A. pubescens in South America is more closely related to A. frontipilis and species of Metzgeria from South America than to any A. pubescens from the Northern Hemisphere. Thus, A. pubescens is Holarctic in distribution and morphologically similar plants form a divergent lineage in South America. Our results do not support Apometzgeria as a separate genus in the Metzgeriaceae.