[Objective] This study aimed to analyze the genetic polymorphism of 39 cassava varieties (lines) preserved in Guangxi Zhuang Autonomous Region Research Institute for Subtropical Crops. [Method] ISSR primers with good polymorphisms and amplification effects in cassava were selected for PCR amplification of 39 cassava germplasms, statistics and analysis of the amplified bands were conducted. In addition, cluster analysis was conducted by using UPGMA method based on the genetic similarity among cassava varieties (lines). [Result] Ten pairs of ISSR primers were selected. A total of 70 clear electrophoretic bands were amplified, each pair of primers had amplified 3-9 electrophoretic bands, with an average of 7, and the length of amplified bands ranged from 150 to 2,000 bp; cluster analysis showed that 39 cassava varieties (lines) were clustered into two categories by the similarity coefficient of 0.67; in addition, the genetic distance among cassava was very narrow, with genetic similarity coefficients ranging between 0.80 and 1.00. [Conclusion] This study laid foundation for breeding of high-quality cassava in China. [Objective] This study aimed to analyze the genetic polymorphism of 39 cassava varieties (lines) preserved in Guangxi Zhuang Autonomous Region Research Institute for Subtropical Crops. [Method] ISSR primers with good polymorphisms and amplification effects in cassava were selected for PCR amplification of 39 In addition, cluster analysis was conducted by using UPGMA method based on the genetic similarity among cassava varieties (lines). [Result] Ten pairs of ISSR primers were selected. A total of 70 clear electrophoretic bands were amplified, each pair of primers had amplified 3-9 electrophoretic bands, with an average of 7, and the length of amplified bands ranged from 150 to 2,000 bp; cluster analysis showed that 39 cassava varieties (lines) were clustered into two categories by the similarity coefficient of 0.67; in addition, the genetic distance among cassava was very narrow, with genetic similarity coefficients ranging between 0.80 and 1.00. [Conclusion] This study laid foundation for breeding of high-quality cassava in China.