Abstract: Arundo donax is a promising crop for bioenergy as it is fast growing, stress-tolerant and high in protein content. The morphological characteristics and biomass yields of A. donax species originated from Yantai, Shandong and Fuzhou, Fujian were compared. Transcriptome analysis in the leaf RNA of both species were conducted by Illumina sequencing. Their expression levels were calculated, and differently expressed genes screened and annotated with databases from sources including Gene Ontology (GO), euKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Further analyses on the signal pathways, such as carbon fixation in photosynthetic organisms, starch and sucrose metabolism and phenylpropanoid biosynthesis, showed significant differences on the expressions of some key enzymes in them. The results provided a useful clue in selecting and breeding A. donax for bioenergy.