Water chestnut Trapa is abundant in lakes of mid-lower reaches of Yangzte River.
Three taxa (T. quadrispinosa, T. japonica and T. bispinosa) were analyzed with AFLP.
The three Trapa taxa formed genetically distinct groups.
Genetic depauperation and evident population structure were found within each taxon.
Each taxon should be separately preserved based on genetic and geographic origin.