Sexual reproduction is often considered essential for evolutionary change, with many plants possessing mechanisms to promote outcrossing and produce genetically variable offspring. Many plant species, however, are also capable of asexual reproduction, but its relative role in population dynamics is often overlooked. Given that sexual reproduction depends in part on mate availability and therefore plant density, would asexual reproduction predominate in rare species, especially those found in highly disturbed habitats? To explore this question, we used field and genetic techniques to investigate the reproductive system of a rare, clonal shrub, Spiraea virginiana Britton, which inhabits the frequently disturbed riparian zone. We performed controlled hand pollinations within and among individuals both within and across populations. We also quantified allelic richness and heterozygosity at a locus purported to control self-incompatibility (SI). Hand pollinations resulted in low total fruit production but more infructescences were produced with outcross pollen (20%) than with self-pollen (2.3%). Low allelic richness (2–7 alleles/population) was found at the putative SI-locus; variation at this locus did not correspond directly with the pollination results, suggesting either the SI system is leaky or that the examined SI-locus is not primarily responsible for incompatibility in this species. This study shows that rarity combined with clonality within a highly disturbed habitat may promote a combination of asexual and sexual reproduction. Although sexual reproduction can occur, it may be limited by a scarcity of available mates for S. virginiana, thereby resulting in primarily asexual reproduction in the species.