Premise of research. Many plant species balance resource allocation between sexual and asexual reproduction. Ecological factors that alter this balance can have important effects on plant populations. By eliminating flowers, floral herbivory (florivory) reduces sexual reproduction and consequently shifts reproductive allocation toward asexual reproduction. Over time, the clonal structure of the population may change. To investigate long-term effects of florivory, we characterized clonal structure in patches of the woodland herb Clintonia borealis (Liliaceae), or the bluebead lily. Methodology. A common understory species of North American boreal forests, bluebead lily is a favorite spring food of Odocoileus virginianus, or white-tailed deer. We sampled patches of bluebead lily located on islands in the Great Lakes, which either had or did not have white-tailed deer. Genotyping using newly developed microsatellite markers allowed clones to be identified. Pivotal results. The clonal structure, measured as the genet-to-ramet ratio (G∶N) of a patch, averaged 0.104 genets per ramet on islands with deer, compared with 0.458 genets per ramet on islands without deer. The difference was significant, based on a linear mixed effects model (∆AICc = 3:94, Akaike weight = 0.878), and the effect size, as measured by Cohen’s d was 1.995. We also observed significantly lower clonal diversity and clonal evenness on islands with deer, which in turn could further limit sexual reproduction due to self-sterility or inbreeding. Conclusions. While the effects of white-tailed deer on plant community structure have been well documented, our results suggest that they may also have significant effects on the reproductive dynamics of individual plant species.