The genetic diversity of forty seven originated from nine countries/regions were analyzed using SCoT molecular marker and the efficiency of SCoT marker in pineapple study was also discussed. Results showed that SCoT has the plenty polymorphsim in pineapple, the percentage of polymorphism bands ranged from 30%-100% and the mean value was 85.37%. The mean value for effective number of alleles, Nei’s gene diversity, Shannon’s information index and polymorphism information content was 1.45, 0.27, 0.41and 0.28, respectively, which suggested that SCoT has the high efficiency on detecting polymorphism in pineapple. Based on the genetic similarity coefficient between pineapple germplasm generated from SCoT markers, all the germplasms were divided into six groups. The first three larger group were groupⅠ, groupⅡand group Ⅲ, which account for 80.85% of the total pineapple germplasm. Although results obtained by principal component analysis was incomplete with that obtained by cluster analysis, the genetic relationship between pineapple germplasm illustrated with the two methods was roughly consistent. All these results would provide the important theoretical basis for the identification, protection and scientific utilization of pineapple in China.