The last decade has seen tremendous growth and interest in renewable energy and fuels aimed primarily at addressing issues of climate change, energy security, and rising energy costs. These efforts coupled with the demand for efficient utilization of biomass place a premium on the detailed analysis of the fundamental chemical structures of biomass, especially in light of the ever-increasing efforts to generate transgenic plants with reduced recalcitrance and altered lignin structure. This review examines the growing application of phosphitylation followed by 31P NMR to quantitatively analyze biomass lignin structures including guaiacyl, syringyl, guaiacyl with carbon substituents at the C5 position, catechol, p–hydroxyphenyl, aliphatic and carboxylic hydroxyl groups. The application of this methodology to provide a rapid analytical tool for lignin/biomass derived bio-oils and biodiesel precursors is also discussed. Utilizing lignin isolated from native and transgenic plants as well as from pretreatment and biological/thermal deconstruction processes, researchers have demonstrated that this technique has unique characterization capabilities which have broad applicability in the biofuels research community.