Determining the phylogenetic and biogeographic distribution of physical dormancy remains a major challenge in germination ecology. Here, our goal was to describe a novel water-impermeable seed coat mechanism causing physical dormancy (PY) in the seeds of Chaetostoma armatum (Melastomataceae). Although seed coat permeability tests indicated a significant increase in seed weight after soaking in distilled water, anatomical and dye-tracking analyses showed that both water and dyes penetrated the seed coat but not the embryo, which remained in a dry state. The water and dye penetrated the lumen of the exotestal cells, which have a thin outer periclinal face and thickened secondary walls with U-shaped phenolic compounds. Because of this structure, water and dye do not penetrate the inner periclinal face of the exotestal cells, indicating PY. Puncturing the seeds increased germination more than tenfold compared to that of the control, but GA3 did not increase germination further. A significant fraction of the seeds did not germinate after puncturing, indicating that embryos are also physiologically dormant (PD). This paper constitutes the first report of the water-impermeable seed coat in the Myrtales and the first report of physiophysical (PD+PY) dormancy in a shrub from a tropical montane area.