AFLP fingerprinting of the 98 main sweetpotato varieties planted in China has been constructed. Using 17 AFLP primer combinations which were selected from 1 208 primer combinations and generated the most amounts of polymorphic bands, AFLP analysis of the 98 main sweetpotato varieties gave a total of 410 clear polymorphic bands with an average of 24.12 polymorphic bands per primer combination. Each one of the 98 sweetpotato varieties could be clearly distinguished by EcoR I-cta/Mse I-ggc primer combination which generated the most polymorphic bands. AFLP-based genetic distance ranged from 0.0546 to 0.5709 with an average of 0.3799. The dendrogram based on AFLP markers indicated that sweetpotato varieties coming from the same regions or having same parents were clustered in the same groups. Analysis of molecular variance (AMOVA) revealed greater variations within regions (94.08%) than among regions (5.92%). Thus, the genetic variations mainly existed within regions, while the variations among regions were very low in the tested sweetpotato varieties. Significant genetic variations existed between “Northern”and “Southern”sweetpotato varieties when Yangtze River was used as the dividing line. AFLP fingerprinting of the 98 sweetpotato varieties planted in China has been constructed. 17 AFLP primer combinations which were selected from 1 208 primer combinations and generated the most amounts of polymorphic bands, AFLP analysis of the 98 sweetpotato varieties gave a total of 410 clear one polymorphic bands with an average of 24.12 polymorphic bands per primer combination. Each one of the 98 sweetpotato varieties could be clearly distinguished by EcoR I-cta / Mse I-ggc primer combination which generated the most polymorphic bands. AFLP-based genetic distance ranged from 0.0546 to 0.5709 with an average of 0.3799. The dendrogram based on AFLP markers indicated that sweetpotato cells coming from the same regions or having same parents were clustered in the same groups. Analysis of molecular variance (AMOVA) revealed greater variations within regions (94.08 %) than among regions (5.92%). Thus, the genetic variations primarily existed within regions, while the variations Among regions were very low in the tested sweetpotato varieties. Significant genetic variations found between “Northern ” and “Southern ” sweetpotato varieties when Yangtze River was used as the dividing line.