Transition from vegetative to reproductive phase in the plant development process is essential for flowering time, which eventually determines biomass production in the potential energy crop, Miscanthus. A recent study reported a diversity of flowering time and photoperiod responses for the species, implying that there exist allelic variations and interactions among flowering-related genes. To characterize individual gene associated with miscanthus flowering, we profiled whole transcriptomes and tried to explore genes at the genome level in the miscanthus. A kinase-dependent regulatory protein, 14-3-3 which was detected in miscanthus leaf and root with 97 and 98% identity, respectively, with that of corn was reported to play a key role as a regulator in signal transduction pathway. Another acidic protein, casein kinase 2 alpha subunit(CKA2α) which was also detected in miscanthus leaf and root was found to influence photoperiodic flowering in several plants and to have a gene identity of 98.5% from sorghum. An FT(Flowering locus T) gene which induces flowering transition under long day condition was detected only in the miscanthus leaf, which showed 98% identity with the gene from sorghum. Another regulating gene, GI(GIGANTEA) which controls the expression of flowering time genes responding to photoperiod was identified both in the leaf and root tissues. The identified genes will be further characterized by in Silico analysis and by using miscanthus mutants, and finally applied for developing a high-yielding biomass cultivar.