Roots are one of the three fundamental organ systems of vascular plants1, and have roles in anchorage, symbiosis, and nutrient and water uptake2-4. However, the fragmentary nature of the fossil record obscures the origins of roots and makes it difficult to identify when the sole defining characteristic of extant roots—the presence of self-renewing structures called root meristems that are covered by a root cap at their apex1-9—evolved. Here we report the discovery of what are—to our knowledge—the oldest meristems of rooting axes, found in the earliest-preserved terrestrial ecosystem10 (the 407-million-year-old Rhynie chert). These meristems, which belonged to the lycopsid Asteroxylon mackiei11-14, lacked root caps and instead developed a continuous epidermis over the surface of the meristem. The rooting axes and meristems of A. mackiei are unique among vascular plants. These data support the hypothesis that roots, as defined in extant vascular plants by the presence of a root cap7, were a late innovation in the vascular lineage. Roots therefore acquired traits in a stepwise fashion. The relatively late origin in lycophytes of roots with caps is consistent with the hypothesis that roots evolved multiple times2 rather than having a single origin1, and the extensive similarities between lycophyte and euphyllophyte roots15-18 therefore represent examples of convergent evolution. The key phylogenetic position of A. mackiei—with its transitional rooting organ—between early diverging land plants that lacked roots and derived plants that developed roots demonstrates how roots were `assembled' during the course of plant evolution.