The San Francisco Volcanic Field is one of the dominant volcanic fields on the Colorado Plateau, and its four million-year volcanic history has created a dramatic substrate age gradient. Sites within Pinyon-Juniper woodlands of the volcanic field share similar climate, elevation, and geology yet display dramatically different chemical and structural soil characteristics. The relative degree of soil development associated with ecosystem age strongly influences both the spatial distribution and composition of the local flora. A multiple response permutation procedure indicated that two distinct floristic assemblages occur; one in substrates younger than 150,000 years and one in older substrates. Indicator species analysis revealed that shrubs dominated younger, coarser, poorly developed volcanic soils while grasses and perennial herbs dominated older, finer, more nutrient-rich soils. Younger substrates harbored a higher degree of endemism, and species richness was positively correlated with ecosystem age.