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In Taiwan, Miscanthus floridulus/sinensis complex displayed the continuous morphological shifting affecting by adaptive divergence with gene flow in incipient speciation.In this study,we analyses genomic divergence within the Miscanthus floridulus/sinensis complex, which reveals various phenotypic and ecological differences in spite of a recent divergence (～1.59million years ago) using multilocus technique.Higher gene flow arisen between sympatric,interspecific populations than between allopatric, intraspecific populations.