Qin, Y., Kabir, M. A., Wang, H. W., Lee, Y. H., Hong, S. H., Kim, J. Y., Yook, M. J., Kim, D. S., Kim, C. S., Kwon, H. and Kim, W. 2013. Assessment of genetic diversity and relationships based on RAPD and AFLP analyses inMiscanthusgenera landraces. Can. J. Plant Sci. 93: 171-182. In this study, molecular markers, random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) as well as combined RAPD and AFLP analysis were used to assess genetic diversity in a reference set of 38 Miscanthus accessions of which 32 were collected from South Korea and 6 from foreign countries. Using 30 selected RAPD primers, 197 amplified products were generated with an average of 6.6 bands, of which 135 bands were polymorphic (68.6%). A total of 1150 bands were detected by four-primer AFLP combinations with an average of 287.5 bands, out of which 923 bands were polymorphic (80.3%) across all the accessions. Analysis of molecular variance (AMOVA) indicated that a high proportion of the genetic variation (56% for RAPD and 58% for AFLP) was found among the Miscanthus species in South Korea. Genetic relationship was estimated using the Jaccard's coefficient values between different accessions, ranging from 0.23 to 0.93 in RAPD and 0.34 to 0.94 in AFLP. The un-weighted pair group method with arithmetic mean (UPGMA) analysis demonstrated less difference between RAPD and AFLP when alternative similarity coefficient was applied. The principal coordinates (PCO) analysis also revealed the significant geographic structure in the tested accessions. Among the accessions, SNU-M-040, 074 and 157 were highly divergent. Pattern of isolation by distance was observed in Miscanthus accessions, indicating that significant genetic differentiation among accessions might be due to the geographic distance.