Lignin is the aromatic biopolymer deposited in the secondary plant cell wall, and is considered as the promising source of the valuable phenolic compounds. There are emerging interests to characterize valuable phenolic compounds from the highly polymeric lignin by applying chemical and biological modification. Despite its significance, the structural analysis of the lignin remains unambiguous. One of the largest obstacle to analyze lignin is its complexity of linkage. The lignin consists three different monomers units linked to each other by diverse linkage types with multiple nodes, often resulting in branching and cycling structure. Our group is developing analytical methods to effectively identify and quantify the complex lignin. For monomers and its derivatives, we developed a LC-UV-MS/MS method for specific detection, identification and quantification. For dimers and more complex lignin, we’re developing a multistage MS method to systematically elucidate the structure.