Genetic diversity among eleven geographic populations of Conogethes punctiferalis in China was investigated using InterSimple Sequence Repeat (ISSR) markers in this study. Six of the 34 used primers were chosen for our ISSR polymorphic analysis. The results showed that 209 bands were polymorphic, making up 99.05% of the total 211 amplified bands. The genetic distances between different C. punctiferalis populations were 0.0059-0.0237. The Nei’s index, Shannon information index, and coefficient of genetic (gene) differentiation among populations (G_st) was 0.1750, 0.2966 and 0.053, respectively, and the estimated value of gene flow from G_st was 8.8724. The results suggest that C. punctiferalis populations in China keep a low level of population genetic differentiation due to a considerable gene flow.