Lily (Lilium) is one of the most beautiful and popular flowers in the world as well as in Vietnam. With the increasing demand of kinds and colors for this flower, scientists have been continuously selecting and creating new lily varieties from available ones. The Vietnamese also has conducted this work as a first step in the collection and field assay; however there are few results on evaluating the diversity of lily varieties to serve for the breeding. Therefore, this paper presents some important results in the study of genetic diversity and genetic relationship of 11 imported and 2 domestic lily varieties by using ISSR (Inter Simple Sequence Repeat) molecular markers. Research showed that PIC (Polymorphic Information Content) values between locus locations ranged from 0.6954 (ISSR 5) to 0.886 (ISSR 56) and the average was 0.82. The result also showed that there were 574 polymorphic segments in a total of 613 segments obtained and the average was 52 polymorphic ones per primer. The coefficient of genetic similarity between each two breeds ranged from 0.30.79. The 13 lily varieties studied were classified into three groups based on similarity coefficient and divided into 4 groups based on PCA (Principal Coordinate Analysis).