Duckweeds are a family of aquatic flowering plants that have a high potential for environmental remediation and biofuel manufacture. Two hundred and twenty clones of duckweeds were collected in Hainan Island, China. Based on morphological and phylogenetic analyses of the chloroplast ribosomal protein S16 intron (rps16) and atpF-atpH intergenic spacer sequences, these clones were classified into four species belonging to four genera: Lemna aequinoctialis, Spirodela polyrhiza, Wolffia globosa, and Landoltia punctata. Eight community types including single-, bi-, and/or tri-species communities were observed. L. aequinoctialis was the most widely distributed of the four species. W. globosa has the highest genetic diversity followed by L. aequinoctialis, whereas S. polyrhiza and L. punctata did not show any significant diversity. Duckweeds collected from the south of Hainan had higher diversity than those from the north. Moreover, very high rates of transversional nucleotide substitutions were found in the rps16 sequences of L. aequinoctialis and W. globosa, which make these duckweeds special with respect to nucleotide substitutions. Keywords Duckweed * Lemnaceae * Single nucleotide polymorphism * Haplotype diversity * Transversion Hainan