Wolffia Horkel ex Schleid.(Lemnaceae) includes the world’s smallest angiosperms.Morphologically,their bodies are extremely simplified,making classification difficult and long-disputed.No reports about the genetic structure of these clonal-dominant aquatic plants have been published until now.In this study,of 247 samples from 42 populations spanning representative locations in China,two chloroplast haplotypes (glo-cp and un-cp) and 66 amplified fragment length polymorphism genotypes were identified.Based on wide sampling,cpDNA haplotypes,and amplified fragment length polymorphism profiles,we found that there are two genetic lineages (glo- and unlineages) of Wolffia species in China.Genotypic and genetic diversity of Wolffia species are high compared with other clonal plants (Simpson’s index,D =0.97; Nei’s diversity,H =0.1835).Different spatial structure patterns were detected between glo- and un- lineages.Positive autocorrelation at short distances (＜400 km) and slightly negative autocorrelations at larger distances (＞ 1500 km) were detected within the glo-lineage,but no significant spatial genetic structure was detected beyond 100 km within the un-lineage.Overall,spatial genetic analysis of W.globosa revealed significant autocorrelation within short distances,indicating that restricted gene flow might be one of the most important factors in shaping genetic structure.