Abstract: Genetic diversity and relationship among 35 banana germplasms involving 3 genotypes (i.e., AAA, AA and ABB) were studied by using the Inter-Simple Sequence Repeat (ISSR) method.As a result, 6 ISSR primers were selected, 38 bands amplified between 200 bp and 2,000 bp, 27 bands detected for polymorphic DNA, and the percentage of polymorphic DNA 71.05% of polymorphic DNA were found.The genetic distances among the banana cultivars were between 4.30% and 33.33%.A cluster analysis was performed applying the unweighted pair group method on arithmetic averages.The banana germplasms were grouped into 6 clusters based on the genetic distance of 25%.Except for Gongjiao (AA) and Jinfen1 (ABB), which were grouped into Cluster III and IV, respectively, the remaining 33 germplasms were classified into 4 clusters, in which Cluster I contained 22 germplasms from different localities and genetypes (AAA and ABB).All germplasms with genotypes AAA and ABB could not be divided into 2 clusters.There appeared no close genetic relationship among some banana germplasms with same genotypes.The germplasms could be discriminated by the 6 selected primers, and ISSR was considered as an effective method for studying genetic relationship among different banana germplasms resources.