[Objectives]  To investigate the relative abundance of different species of rice stem borers and the genetic diversity of different geographical populations of the pink stem borer, Sesamia inferens (Walker) in rice growing regions of Sichuan-Chongqing, and provide suggestions for the regional management of borer populations. [Methods]  We conducted a field survey during the rice grain-filling stage to determine the relative abundance of different species of rice stem borers in 13 cities in the Sichuan-Chongqing rice growing region and collected S. inferens specimens from 13 geographical populations for genetic analysis. We then sequenced the cytochrome oxidase subunitⅠ(COⅠ) and cytochrome oxidase subunitⅡ(COⅡ) of mitochondrial DNA (mtDNA) of S. inferens specimens from different populations and analyzed their genetic diversity sequence varication with MEGA and DNA Sequence Polymorphism. [Results]  The species of rice stem borer identified in our survey were Chilo suppressalis, Tryporyza incertulas and S. inferens, and the dominant species were C. suppressalis and S. inferens. A 627 bp segment of COⅠ gene from 60 mature S. inferens larvae was sequenced and analyzed, resulting in the identification of 386 variable sites and 16 haplotypes. Haplotype diversity among different populations in eastern Sichuan was 0.910 57. A phylogenetic tree indicates that, with the exception of the YS population, all other populations from eastern Sichuan grouped into one great clade and all other geographic populations grouped into another great clade. Based on the same 60 DNA samples, the length of the COⅡ gene was 363 bp, and 228 variable sites and 10 haplotypes were identified. Haplotype diversity among different eastern Sichuan populations was 0.715 79. A phylogenetic tree showed that the Chongqing city population, Hangzhou population and ZY population grouped into one clade, whereas all other geographic populations grouped into another clade. [Conclusion]  The dominant species of rice stem borer in the Sichuan-Chongqing rice growing region are C. suppressalis and S. inferens. Haplotype diversity based on both COⅠ and COⅡ sequences indicates that there is more haplotype diversity in eastern Sichuan than in other geographical areas. We found little correlation between genetic diversity and geographical populations.