Abstract: The genetic diversity and phylogenetic relationship of 94 yam germplasm was analyzed by ISSR.24 primers were selected from 100 primers and 352 clear strips were amplified.344 clear strips were polymorphic bands and the percentage of polymorphic bands was 97.7%.Genetic cluster analysis indiated that 94 yam germplasm were divided into 4 groups and the genetic distances were Dioscorea(0.053 8-0.088 4),Dioscorea alata(0.035 3-0.068 2),Dioscorea fordii(0.053 3-0.138 2) and Dioscorea persimilis(0.054 2-0.126 6).Based on the genetic similarity and the population,results suggested that Dioscorea alata group had the closest phylogenetic relationship with Dioscorea fordii group,closer with Dioscorea group and farther with Dioscorea persimilis group.