Analysis of 180 accessions of Miscanthus using a DArT platform revealed high diversity. The phylogenetic analysis revealed that M. × giganteus accessions fall into two genetically distinct groups. Miscanthus is a genus of perennial rhizomatous grasses that has emerged in last 20 years as a feedstock for bioenergy and biofuel production. Currently, the most widely used accession for bioenergy purposes is Miscanthus × giganteus, a sterile triploid hybrid between Miscanthus sinensis and Miscanthus sacchariflorus. However, previous reports have shown that genetic diversity of Miscanthus × giganteus is limited. Here, we report development of Diversity Arrays Technology platform for the analysis of genetic structure of a Miscanthus collection of 180 accessions. A total of 906 markers were obtained of which around 25.5% exhibited polymorphism information content value in the range of 0.40 and 0.50 and are considered particularly informative. Newly developed marker system will serve as an additional resource to assist crop improvement, germplasm preservation and genetic studies. Three types of analysis indicated that 180 accessions from the collection were well differentiated and presented high diversity. Interestingly, the analysis revealed that there are two separate groups of plants, significantly differing in genetic diversity, that are commercially available as M. × giganteus. We suggest that one of these groups is most likely mutants or somaclonal variants of original M. × giganteus. The other group is recent hybrids of Miscanthus of higher genetic diversity. This study indicates that the diversity of commercially available M. × giganteus is higher than commonly assumed. Development of the new marker system can significantly assist breeding of new commercial cultivars of Miscanthus for bioenergy use.