Effective conservation strategies for rare clonal plant species require knowledge of their population-level genetic diversity. We used data from genetic markers (Inter-Simple Sequence Repeat (ISSR), and Sequence Characterized Amplified Region (SCAR)) to estimate the number of genetically distinct individuals and the spatial extent of such genets within study populations of the federally endangered Alabama leather flower (Clematis socialis). We found high clonal diversity in C. socialis in spite of the limited seed set and seedling recruitment previously reported for this species. ISSR analyses of plants from the six known populations of C. socialis yielded 54 distinct multilocus genotypes from 74 sampled plants. Although the populations are separated by an average of 60 km, related genotypes were relatively evenly distributed among all populations. Within populations, the majority of C. socialis genets extended less than 1 m in diameter, but two large individuals spanning 11 m were identified. Based on observed growth data, the 11 m result suggests that C. socialis genets can live for at least 55 years. The size and relative longevity of C. socialis genets have likely slowed the loss of genetic diversity in this rare, clonal species. Additionally, we estimate that population loss and fragmentation of C. socialis populations have been relatively recent: within two to three generations. Finally, our data indicate that without sexual reproduction, rare genets are likely to go extinct and genetic diversity will decline unless populations are managed to prevent this outcome. In order for conserved populations to persist, research on how management activities simultaneously affect sexual and clonal reproduction in these populations is necessary.