[Objectives]  To investigate whether or not transgenic rice will affect the genetic diversity of Chilo suppressalis (Walker). [Methods]  12 individuals of C. suppressalis were randomly selected respectively from specimens collected in Jiangxi and Hunan. After extraction of genomic DNA, PCR and cloning of 658 bp fragment from the COⅠgene ( 35 - 692 bp), 158 clones were sequenced. Meanwhile three worms were analyzed by PCR-DGGE. [Results]  173 polymorphic sites were identified in the 658 bp fragment. The haplotype diversity (h) of Jiangxi samples was 0.820 whereas that of Hunan samples was only 0.542, suggesting greater COⅠ gene polymorphism in Jiangxi than Hunan population. DGGE analysis of a 266-bp-fragment in the COⅠ gene (1 278-1 493 bp) resulted in five distinct bands. Three worms could be clustered into two groups, which is consistent with result of gene sequencing. [Conclusion]  Sequencing can obtain more detailed information on the genetic diversity of target genes in C. suppressalis but is higher in cost and is relatively time consuming. DGGE provides less information but is a high-throughput method. If the DGGE system is well optimized and used properly, large numbers of samples can be analyzed in a reasonable period of time. So DGGE is suitable for investigating whether or not transgenic rice will affect the population genetic diversity of target insects, i.e. C. suppressalis, and non-target insect, i.e. rice plant hoppers.