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Miscanthus lutarioriparius is an endemic species in China and has been widely accepted as a promising eco-bioindustrial plant. Currently, predominantly used germplasms have narrow genetic diversity, which causes a gene resource utilization plateau. Therefore, this study was designed to map the geographic and genetic distribution of M. lutarioriparius. Grid search tuning technique was applied to combine occurrence sites, which was followed by the genetic diversity analysis using the Simple Sequence Repeat markers. The results have revealed that the natural distribution of M. lutarioriparius is in the area with altitude less than 300 m and enclosed by the eastern line of East China Sea, western boundary along the longitude line of 111° E, northern boundary of the Qinling-Huai River line, and the southern line of the 27–28° N in Hunan and Jiangxi, and the 30° N line in Zhejiang. The further analysis has demonstrated that the northern line is mainly determined by the climatic factors, whereas the other three boundaries by the dispersal barriers of the sea and high mountains. The genetic diversity of M. lutarioriparius across its distribution range is high with a total Nei's genetic diversity of 0.2462. Populations from the downstream of the Yangtze River generally have a higher genetic diversity than the relative upstream areas. The centeres of genetic diversity for the M. lutarioriparius across China are located in the central and the southern Jiangsu. Outcomes of this study will help expanding the M. lutarioriparius cultivation through improving breeding and subsequently accelerate the development of biobased industry. • Exact distribution range of M. lutarioriparius across China was firstly mapped. • Spatial distribution of M. lutarioriparius genetic variation was mapped. • M. lutarioriparius has a high genetic diversity than that of other monocots. • Key for the development of future biobased industry. • Central and southern Jiangsu are centers of M. lutarioriparius genetic variation. [ABSTRACT FROM AUTHOR]