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For the plants with important ecological or economic values, understanding the genetic structure of their populations is crucial to inform conservation strategies. Chinese wild rice Zizania latifolia is distributed in the East China along a wide stretch of latitudinal zones (20 degrees-51 degrees N). In this study, using restriction-site associated DNA sequencing (RAD-seq), the genetic structure and local adaptation were evaluated on 60 wild samples composed of 10 Z. latifolia populations collected along a latitudinal gradient and 6 cultivated samples from different cultivars in central China. Low levels of genetic variability were found in the Z. latifolia populations (HE = 0.08-1.52). Population structure analysis showed that samples firstly divided into two major clusters (north and south groups), splitting along a temperature boundary. It was estimated that the two groups diverged during the 8.2 kiloyear event and later experienced severe genetic bottlenecks with advancement of agriculture and increase in human population 2k years later. Compared to geographical distance, environment had a higher contribution to allele frequency variations (r2=0.3467, P G 0.001 vs r2=0.4702, P G 0.001) and morphological variations of populations (r2=0.6110, P G 0.001 vs r2=0.7739, P G 0.001). Several loci were found to be correlated with environmental variables as well as morphological traits, most of which were annotated as retrotransposons. Considering the abundance of transposable elements in the Z. latifolia genome, differentiation and local adaptation was inferred to be partly driven by temperature-induced transposable elements activity. Based on these results, populations from different latitude zones should be separately protected due to their high genetic differentiation and local adaptation.