Climate change has the potential to alter the genetic diversity of plant populations with consequences for ecosystem function. In this study we addressed whether a long-term climate change manipulation has altered the genetic diversity of a dominant C4 grass, Andropogon gerardii, which contributes disproportionately to ecosystem productivity in the tallgrass prairie, using the Rainfall Manipulation Plots (RaMPs). We compared the genetic diversity and genotypic structure found in the altered (increased rainfall variability) and ambient RaMPs with reference plots created in unmaniuplated prairie. We found a decade of altered rainfall patterns in the RaMPs significantly altered both genotypic structure and genetic diversity of A. gerardii. Genotypic richness, evenness, and diversity were reduced in the altered RaMPs, whereas the ambient RaMPs treatment had only reduced genotypic evenness. In addition, we found individuals in the ambient RaMPs and reference plots were significantly more closely related to one another than is expected from random, whereas, individuals in the altered RaMPs did not differ from a random distribution indicating greater genetic diversity. Our results suggest that despite a reduction of number of A. gerardii genotypes with the altered precipitation treatment, these remaining genotypes are less related to each other. This increase in genetic diversity may be the result of diversifying selection. Moreover, increased genetic diversity could have important consequences for ecosystem functioning, as we have found genetic diversity positively correlates with aboveground productivity in this system.