Abstract: Using ISSR molecular markers, PCR products of 36 guava germplasms were purified by polyacrylamide gel electrophoresis and photographed the images for a UPGMA analysis to establish the genetic relationship. Out of 100 UBC series ISSR primers, 9 rich and stable polymorphic primers were selected and 165 bands amplified. Among the 165 bands, 129 were polymorphic rendering a polymorphism percentage of 78.18%. The amplified results could satisfactorily distinguish the 36 germplasms. The genetic similarity coefficient of all samples ranged from 0.70 to 0.93, averaging 0.815. At the coefficient of 0.75, the 36 germplasms were divided into 4 groups. The results were consistent with the morphological classification. Although the genetic basis for classification was weak, with the aid of ISSR molecular markers, clear identifications for the individual germplasms of the collection were obtained.