Although capable of sexual reproduction, many plants also rely heavily on clonal reproduction. The formation of multiple, physiologically-independent units with the same genotype has important implications for spatial genetic structure and genetic diversity in these plants. The endangered scrub-dwelling perennial, Polygonella myriophylla is known to reproduce both sexually and clonally but no study to date has been able to investigate the spatial genetic patterns that occur in this species. I use microsatellite markers to investigate questions about clonal structure and genetic diversity in five populations of P. myriophylla and address some of the implications of my findings for conservation of this species: Overall, I find that 57% of sampled clusters of P. myriophylla are composed of a single genet (genetic individual) with multiple physiological units (ramets) while the remainder are made up of two or more genets. I found differences in both clonal reproduction and genetic diversity among populations. I also found evidence of limited gene flow even over small spatial scales (less than 10 km) and for at least 4 genetic clusters occurring within the species range. Despite high levels of genetic diversity overall, there is evidence of reduced genetic diversity in two populations My results suggest that high levels of clonality may be important in maintaining genetic diversity in P. myriophylla. I also provide evidence that dirt roadsides may not represent a refuge for this species.