Wyethia reticulata is an edaphic endemic in the Sierra Nevada foothills. Its sympatric congener, W. bolanderi, is also restricted to the foothills, but has a north-south range of 275 km, compared to 14 km for W. reticulata. The goals of this study were to determine clonal diversity, population size, genetic variation, and spatial and generic structure for each species from paired populations in El Dorado County, California, using allozyme and RAPD (random amplified polymorphic DNA) methodologies. Wyethia reticulata, spreading by rhizomes, had populations dominated by a few large individuals, while W. bolanderi, with a basal caudex, had populations of a few hundred evenly sized individuals. Genetic analyses indicated that W. reticulata, compared to its congener, had somewhat less genetic diversity (H(T): 0.28 vs. 0.38), had more of its genetic variation partitioned among populations (F(ST): 0.25 vs. 0.07), and showed a complete absence of inbreeding (F(IS): -0.03 vs. 0.22). Population membership in accord with populations defined by geographical location resulted only when all markers were included in the analysis. Ecological limits on recruitment of genets appears to result in small population size in W. reticulata. Limited gene flow, drift within small populations, and sexual reproductive dominance of large clones result in the genetic divergence of populations in this species, while genetic diversity is maintained by the longevity of clones and outbreeding.