Given the drastic decline in biodiversity at all levels, it is imperative that we consider the potential affects of diversity within single species on ecosystem functioning. However, empirical data describing the relationship between intraspecific diversity and ecosystem functioning are lacking. We present field data demonstrating that the litter phenotype of individual trees affects carbon and nitrogen fluxes during decomposition and that single phenotype treatments differ in ecosystem processes from a phenotypic mix. Since nutrient dynamics are related to the chemistry of the litter, we then use the strength of the relationship between genetic distance and litter chemistry to infer the existence of genotypic effects on ecosystem functioning. In combination, our field results provide the first evidence that losses in intraspecific diversity can affect the ecosystem processes of carbon and nitrogen cycling. We also present results from an experiment that simulated both a decline in biodiversity and an increase in nitrogen deposition. In soil microcosms, we tested effects of variation in intraspecific litter diversity and nitrogen deposition on soil respiration and nitrogen leaching. Increases in intraspecific litter diversity increased soil respiration overall, with the greatest increases in respiration occurring under high nitrogen deposition. Our results demonstrate the potential for losses in genetic diversity to interact with other global environmental changes to influence terrestrial nutrient cycles We used a second microcosm experiment to determine whether the intraspecific diversity effects of turkey oak leaf litter on nutrient dynamics would be masked by the presence of naturally co-occurring longleaf pine litter. We varied the phenotypic diversity of oak litter in the presence and absence of pine litter and measured fluxes of carbon and nitrogen over a 42 week period. Soil C:N ratio peaked at intermediate levels of oak phenotypic diversity whereas the total amount of DOC leached from microcosms declined as oak phenotypic diversity increased. In no case did the presence or absence of pine litter influence the response of nutrient fluxes to changes in oak litter diversity. Our results indicate that phenotypic diversity can be important even in the presence of another species, and suggest that conservation efforts should consider both inter- and intraspecific diversity.