Inter-simple sequence repeat (ISSR) markers were used to construct DNA fingerprint patterns and molecular identity of Brasenia schreberi germplasm,an endangered aquatic plant in China.The result of UPGMA cluster analyses showed that three B.schreberi populations (SDS,HZD,HZC) from East China were clearly separated from the three populations (LCZ,LCF,LCY) from Central China.The UPGMA cluster analysis of 46 individuals of B.schreberi showed that samples from the same geographical region (Central China or East China) formed a group,whereas samples from different regions were separated.Three core ISSR primers (P817,P825,P845) can be used to amplify the special band-patterns of two B. schreberi varieties (SuHang and Lichuan),and therefore can be used for establishing molecular identity of B.schreberi germlasm.The differentiation at the molecular level of B.schreberi germlasm is consistent with their geographical isolation and diversity climate zone.It is recommend that the use of a variety of molecular markers to construct a molecular ID card database of different B.schreberi species,combined with the characteristics of traditional traits,will facilitate the more accurate identification of B.schreberi varieties resources.