Genetic diversity of 3 populations of Staphylea bumalda that sampled from Hubei, Anhui and Henan was detected by employing amplified fragment length polymorphism (AFLP) markers. 489 clear bands were amplified with 4 pairs of primer and 460 (93.99%) of them were polymorphic. Nei’s gene diversity and Shannon’s information index ranged from 0.1920 to 0.2046 and from 0.2937 to 0.3151, respectively. The highest population genetic diversity was Dawu from Hubei Province. Nei’s gene diversity for the species and population were 0.2190 and 0.1964, respectively. The analysis of variance showed that the main variance within populations was 89.68%. The mean genetic distance among the 3 population was 0.0292. The results of UPGMA cluster analysis based on genetic distance revealed there was high genetic similarity between the population and the genetic distance was closely related to its distribution area. The research suggests that the important way for Staphylea bumalda conservation will be conserving the high genetic diversity populations.