Analysis of the genetic diversity of Miscanthus, a representative crop associated with bioenergy, is necessary for the enhancement of Miscanthus biomass production, an important and challenging research prospect. This study was conducted to determine the genetic diversity of Miscanthus accessions, with regard to geographical location. Inter-simple sequence repeat (ISSR) and random amplified polymorphic DNA (RAPD) markers were used to assess the relationships among, and genetic diversity of, 24 Miscanthus accessions collected from the USA and China. These 24 Miscanthus accessions were all shown to be diploid by flow cytometry. Using 30 selected ISSR primers, a total of 96 amplified products were produced, with a mean of 11 products per primer, and the polymorphism percentage was 70%. Using 11 primers, the RAPD method produced 194 amplified products, and the polymorphism percentage was 83% in all accessions. The genetic distance was 0.36–0.71, according to Jaccard’s coefficient for combined ISSR and RAPD data. The 24 Miscanthus accessions were classified into two groups (USA and China) through UPGMA clustering analysis. This classification revealed significant genetic diversity among Miscanthus accessions according to geographical location. Future efforts to analyze genetic diversity will facilitate the improvement of biomass characteristics in other grasses undergoing development as energy crops.
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