Miscanthus is a potential bioenergy crop due to its C-4 perennial growth, rhizomatous propagation, and relatively great resistance to abiotic stress. To obtain genetic diversity for future breeding program, we collected over 69 accessions of miscanthus germplasm from Korea and other East Asian regions and performed morphology-based phenotyping and SSR-based genotyping. There are two distinctive species groups, Miscanthus sinensis and Miscanthus sacchariflorus, the most considered two parental candidates for breeding of high yield cultivars, in both morphological trait and SSR marker analyses. Among 14 morphological traits, we found that three major traits, namely the presence of awn in spikelet, the ratio between the callus hair and spikelet, and new shoot emergence in autumn. In addition, a total of 164 amplicons generated from 31 SSR primer pairs, which were selected out of 122 SSRs, were used to cluster and evaluate the genetic variation and relationships among 69 accessions. The accessions were classified by species followed by region in SSR analysis. Our results suggested that phylogenetic analyses using morphological traits and SSR markers are effective for the diversity assessment and identification of phylogenic groups of Miscanthus species. This phylogenetic group based on morphological traits and SSR markers will provide effective parental selection for future breeding of a highly productive miscanthus cultivar. However, the inconsistency between phylogenic trees using morphological traits and SSR analyses requires further studies using additional SSR markers derived from the miscanthus genome sequence to provide better insight and understanding of the genetic diversity of miscanthus. (C) 2014 Elsevier Ltd. All rights reserved.