Miscanthus is one of the important crops for bioenergy feedstock. Applicable molecular makers would be useful for development of valuable cultivar with enhanced biomass. Microsatellites as a co-dominant are widely useful for many applications in plant genetics and breeding such as genetic diversity analysis, cultivar identification, and marker-assisted selection. In order to develop novel EST-SSR markers for genetic improvement, we obtained the EST sequence data from the constructed cDNA libraries using a leaf and rhizome organs in the M.sinensis and M.sacchariflorus. SSR motifs were identified by SSR search-module program SciRoKo software. The number of SSR motifs was 1,724 in M.sinensis (leaf: 948, rhizome: 776) and 1,158 in M.sacchariflorus (leaf: 549, rhizome: 609). The most common repeat was tri-nucleotide followed by tetra-, di-, penta-nucleotide. CCG and AGC motifs were detected the most abundant repeat type in tri-nucleotide. We used an ORF Predictor program to screen the SSR location in the genome. The majority of the motifs were located in the ORF regions than the untranslated regions (UTRs). Especially, the tri-nucleotide was localized in the ORF regions, whereas di- and tetra-nucleotide were frequent in UTR regions. Based on SSR-containing sequence of the M.sinensis (leaf), 228 primer pairs were designed using Primer3 program. Randomly selected 20 primer pair was firstly screened using genomic DNA for their effectiveness to amplify SSR fragments of the expected size and to detect allele polymorphism. Fourteen out of total twenty primer pairs (70%) were successfully amplified. The remaining SSRs will be further screened and reported. When confirmed, those SSRs will be used for studying genetic diversity of the collected Miscanthus germplasm.