Utilizing 11 stands of cottonwood forest in northern Utah that vary in average plant heterozygosity, we addressed the hypothesis that high above-ground genetic diversity would result in high below-ground microbial diversity. We found that soil nitrogen availability is related to stand heterozygosity, explaining 63% of the variation in soil ammonium. While we found a significant relationship between stand heterozygosity and microbial diversity, as measured with Phospholipid Fatty Acid Analysis (PLFA), we found only weak relationships between heterozygosity and microbial biomass or enzyme activity. These data suggest that tight links exist between above- and below-ground processes, possibly mediated by genetic-based differences in leaf/litter substrate quality. Second, these data support the idea of the importance of genetic variation to both community and ecosystem-level processes.