Abstract: The polymorphism of 17 Pine apple cultivars were analyzed by inter-simple sequence repeat(ISSR).6 primers were selected from 62 ISSR primers, and a total of 70 DNA bands were amplified, 44 of which(62.86%)were polymorphic. The average number of DNA bands amplified by each primer was 11.67. There were specific amplified bands in six cultivars, and these bands can be used in Pine apple identification. The dendrogram constructed by UPGMA showed that the 17 individuals were classified into three groups. Genetic relationships of Pine apple were also discussed.