【Background】Western flower thrips, Frankliniella occidentalis (Pergande), is one of the invasive insect pests occurring in many provinces of China and causing serious economic loss in invaded regions. 【Method】In the present study, intersimple sequence repeat (ISSRPCR) system in F.occidentalis was optimized. Seven factors including template DNA, primers, Taq DNA polymerase, buffer, dNTPs, Mg2+ and deionized formamide were designed with a single factor test, and then the corresponding better concentrations were screened out initially. After that four more influential factors for ISSRPCR system were designed employing orthogonal design test with four levels and four factors, and significance test and variance analysis were employed to analyze the PCR amplification data. 〖JP3〗【Result】The system, containing 30 ng DNA template, 2.0 μL 10×EasyTaq buffer, 1.〖KG-*8〗05 μmol〖KG-*2〗·〖KG-*4〗L-1 primers, 2.0 U EasyTaq DNA polymerase, 〖JP〗212.5 μmol〖KG-*2〗·〖KG-*4〗L-1 dNTPs and 2.25 mmol〖KG-*2〗·〖KG-*4〗L-1 MgSO4 in 20 μL reaction, gave the best results in ISSRPCR system. 【Conclusion and significance】DNA of nine samples of F.occidentalis collected in Kunming, Yuxi, Chuxiong, Honghe, Baoshan, Zhaotong, Lijiang, Dali and Puer in Yunnan Province were used to detect suitability of this ISSRPCR system. The results indicated that the system is suitable for genetic diversity detection of F.occidentalis.