The genetic relationship of 15 apple rootstock germplasms were studied using ISSR markers.Ten pairs of primers were used and a total of 75 bands were yielded,among which 67 were polymorphic.Primers 827,M05 and M08 could be used for effectively genotyping the 15 germplasms.The systematical cluster analysis showed that 15 apple rootstock germplasms could be divided into three groups: Malus , Pyrus and Sorbus with a genetic similarity coefficient of 0.66,which fitted well with the morphological genealogy.