In salt marsh habitats, noted for their extreme environments, a widely held assumption is that a few large clones dominate plant populations. Using a large number of polymorphic genetic markers, we were able to test this assumption for two salt marsh plants known to span extreme salinity gradients. For both species, clonal diversity was surprisingly high across populations: Simpson's diversity indices were 0.96 and 0.99. Although clonal diversity was high, there was no pattern of association between specific clones or alleles with salt microhabitat. Our findings suggest that sexual reproduction and recruitment from seeds may have been generally underappreciated as an important ecological force in the salt marsh. Furthermore, clonal diversity has implications for conservation and restoration of these critical coastal habitats, particularly with regard to buffering environmental change or disease. Recent studies also suggest that high levels of intraspecific diversity can affect a variety of community and ecosystem processes.