Novel fungal endophyte (Neotyphodium coenophialum; Latch, Christensen and Samuels; Glenn, Bacon, and Hanlin) genotypes in symbiosis with tall fescue (Lolium arundinaceum; Schreb. Darbysh.) have been recently introduced to agricultural seed markets. These novel endophytes do not produce the full suite of toxins that the 'common toxic' form does, and therefore, may not have the same consequences on plant and soil processes. Here, we evaluated the effects of endophyte presence and genotype on ecosystem processes of tall fescue stands. We quantified the effects of the presence of the common toxic endophyte (CT), two novel endophyte genotypes (AR-542, AR-584), no endophyte (endophyte free, E-), and a mixture of all endophyte statuses (mix) within a single genotype of tall fescue (PDF) on various soil and plant parameters. Endophyte presence and genotype affected tall fescue cover and plant species diversity: cover-CT, AR-542, AR -584, mix > E- and species diversity-E- > AR-542, AR -584 > CT, mix. Most measured soil parameters had significant endophyte effects. For example, higher fluxes of soil CO2 and N2O were measured from stands of AR-542 than from the other endophyte treatments. These results indicate that endophyte presence and genetic identity are important in understanding the ecosystem-scale effects of this agronomically important grass-fungal symbiosis.