Abstract Sexual reproduction, despite its associated costs and risks, is prevalent among many organisms, presumably to generate and maintain genetic diversity. This diversity is vital for adapting to environmental changes and combating natural enemies. Paradoxically, several clonal species also exhibit high genetic diversity. One theory for the maintenance of this genetic diversity is frequency‐dependent selection, which favours rare genotypes over common ones, limiting the extent and dominance of a single clone, thereby preserving genetic diversity. Empirical evidence for this theory under natural conditions is sparse. Twelve years ago, we established in the forest 14 genetically diverse plots where all plants had a unique genotype (rare genotypes) and paired with them clonal plots where all plants had the same genotype (common genotypes) to test whether common genotypes have a disadvantage and frequency‐dependent selection is in action. Clones were created from cuttings from Piper cordulatum , a naturally clonally reproducing understorey plant. We aimed to test whether common genotypes are disadvantaged and whether frequency‐dependent selection is effective in limiting the dominance of clones and preserving genetic diversity. Over the experiment's first 10 years, herbivory, pathogen attacks and plant size remained similar across both genotype categories. Intriguingly, clones exhibited superior survival during the initial 5 years. Survival rates equalized for rare and common genotypes by the decade's end. By year 12, survival remained similar for rare and common genotypes. However, modelled survival projections based on the 12‐year‐long trend suggest that common genotypes might experience increased mortality in the long run, consistent with the hypothesis of negative frequency‐dependent selection. Moreover, plants in clonal plots exhibited lower fitness in terms of infructescence production at the plot level by the tenth year. Our findings suggest that having low genetic diversity in the neighbourhood does not increase disease or herbivory susceptibility or reduce short‐term survival. The impact of negative frequency‐dependent selection is not immediate. However, it could eventually restrict the survival and reproduction of Piper clones in a tropical forest's understorey, curbing the dominance of any single genotype and potentially maintain genetic diversity. Read the free Plain Language Summary for this article on the Journal blog.