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The genetic diversity among 30 accessions including 18 Erianthus arundinaceus and 12 Saccharum species was analyzed using amplified fragment length polymorphism (AFLP) markers. We obtained 2245 fragments using 16 primer combinations. The Erianthus collection generated 1115 fragments of which 772 (69.2%) were polymorphic. Of the 342 monomorphic fragments (30.8%), 222 were specific to E . arundinaceus. The neighbor‐joining tree based on the detected fragments clearly separated the Erianthus and Saccharum accessions into distinct groups. The Erianthus collection was further subdivided into two Japanese groups and one Indonesian group, with a high level of genetic differentiation among these groups ( F st = 0.2062). These results represent the first molecular characterization of the Japanese E. arundinaceus breeding materials and provide a useful initial resource for breeding to improve the bioenergy potential of Erianthus spp.

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