Using the well-developed microbial system, Clostridium phytofermentans, we have developed a robust bioassay for biomass digestibility and conversion to biofuels. The bioassay can be used to measure the impact of plant genetic diversity on digestibility, and thereby determine the potential effects of altered energy crop traits. Moreover, the use of C. phytofermentans takes into consideration specific organismal interactions, which will be critical in single stage fermentation or consolidated bioprocessing. In order to develop a baseline for our bioassay, we utilized two well characterized lignin mutants of sorghum, brown midrib-6 (bmr-6) and brown midrib-12 (bmr-12) and the double mutant (bmr-6/bmr-12). Lignin, a component of secondary cell walls, is strongly associated with plant tissue recalcitrance to conversion to biofuels. These mutants exhibit a significant reduction in total lignin content and are therefore more digestible. Whole, field grown, de-grained plants were ground to a fine powder and used as a substrate for C. phytofermentans growth. We detected significant differences in ethanol production among the sorghum genotypes by HPLC analysis of three day old anaerobic cultures. We also measured significant variation among different accessions of Arabidopsis thaliana and Brachypodium distachyon. By using C. phytofermentans as an indicator of feedstock quality we can observe differences both within and among species, as well as take into account specific plant-microbe interactions. Ultimately, we will use this assay to study the genetics of plant biofuel properties.