In order to improve efficiency in selecting arrowhead cultivars as parents, to provide guidance in choosing best parent combination for crossing，the genetic diversity was studied in 41 traditional cultivars and 26 wild resources conserved in Wuhan National Germplasm Repository for Aquatic Vegetables. The result showed that the genetic diversity index of all traits were relatively large, the genetic diversity index of quantity traits (1.840-2.039) were higher than quality traits(1.033-1.382), it indicated that these resources had wide genetic diversity, and it was probable to select bigger crom and higher yield variety. Though cluster analyzing based on 13 phenotypic traits, 67 arrowhead germplasm could be classified into 3 categories. The first category was wild resources and could be classified into 3 sub-categories further more. The second category was cultivated yellow arrowhead. The third category was cultivated grey arrowhead and could be classified into 2 sub-categories. The genetic relationship were relatively far between categories or sub-categories. The materials in different categories or sub-categories should be chose as parent while crossing.