Lignin forms complex with cellulose, which inhibits cellulose breakdown in bioethanol production. M. ×giganteus is a suitable material for bioethanol production because of its high yield, and decreasing lignin content will increase its crop value. M. ×giganteus is a triploid sterile plant derived from natural cross between M. sacchariflorus and M. sinensis, and currently only one genotype is cultivated. Recently, three new triploid hybrids between M. sacchariflorus and M. sinensis were discovered from sympatric area of M. sinensis and M. sacchariflorus populations in Kushima, Miyazaki Prefecture, Japan (Nishiwaki et al., 2011). These hybrids possessed different ITS genotypes, and also exhibited differences in the morphological characteristics compared to the presently widely cultivated M. ×giganteus. These materials may also show differences in their lignin content and composition. Eight lignin biosynthesis genes, phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), p-coumarate 3-hydroxylase (C3H), caffeic acid/5-hydroxyferulic acid O-methyltransferase (COMT), 4-coumarate: coenzyme A ligase (4CL), cinnamoyl CoA reductase (CCR), ferulate 5-hydroxylase (F5H), and cinnamyl alcohol dehydrogenase (CAD) were isolated from M. sinensis accession Tanegashima by reverse transcription polymerase chain reaction and rapid amplification of cDNA ends method based on maize, sorghum and sugarcane orthologous genes. Based on the isolated gene sequences, primers for expression analysis were designed. The expression levels of the genes were compared in leaves and stem of the hybrids and M. xgiganteus.