[Aim] Understanding the spread routes and the origin of quarantine pests is important in international trade. Bactrocera cucurbitae is a worldwide quarantine pest and is also included in the Chinese quarantine list. We aimed to study the genetic differences of B.cucurbitae populations intercetped at different customs ports in China by simple sequence repeats (SSR) identified from transcriptome data.[Method] Polymorphic primers were designed based on the SSR obtained from four transcriptomes of B.cucurbitae in different regions by bioinformatics methods. Forty-nine B.cucurbitae samples from eleven provinces/regions of China were selected for verification, and the NTsys and Popgene 32 softwares were used to analyze their genetic diversity.[Result] Fifteen pairs of primers with reliable polymorphism were selected. An UPGMA cluster analysis clustered the populations of Xinjiang, Sichuan and Guangxi into one clade, the populations of Zhejiang clustered with the ones of Guangdong and Jiangsu, and the populations of Shanghai clustered with the ones of Yunnan, Hainan; the populations from Beijing formed a separate cluster.[Conclusion] The genetic differentiation coefficient among populations was 0.6712, indicating that B.cucurbitae populations in different regions have varied genetic background, and these populations might have different original sources. These results provide the theory and technique support to identify the origins of quarantine pests.