The genetic diversity of 21 purple and 28 red and yellow sweetpotato varieties has been evaluated by ISSR markers. There were 138 polymorphic alleles, 89.6% out of 154 amplified loci based on 17 selected ISSR primers with average 8.12 alleles each primer that shown a rich genetic diversity among the population. Clustering and principal component analysis showed that the all 49 sweetpotato clones had been divided into 4 groups with higher genetic distance among groups, and the red and yellow meat types have been ascribed into group Ⅱ. It indicated that there were different evolutionary relationship of purple, red and yellow sweetpotato germplasm. The coefficient of genetic conformability of all varieties were 0.58~0.93, 51.4% of germplasm were 0.61~0.70 and 44.0% of germplasm were 0.71-0.80. There was closer genetic relationship of the varieties come from the same or the nearby regions or breeding institute. It is discussed that how to use these varieties in sweetpotato breeding.