Geographic clines in genetic polymorphisms are widely believed as an evidence of climate change. We hypothesized green peach aphid, Myzus persicae Sulzer, one of the major insect pests in highland chinese cabbage cultivation, may also have some interactions with climate change. As the first step, we tried to find the available markers from six local strains (five collected at different heights in Hoengseong and Pyeongchang area and one from laboratory). A strain from Jeju island was used as an out-group. Although there was no significant difference in sequences of partial ribosomal RNA fragment and mitochondrial cytochrome oxidase I, and esterase isozyme pattern, we found four inter-simple sequence repeat (ISSR) markers in 22 used ISSR primers (+AGA, +CCA, +CGA, CGA+). These primers can be used as good markers to trace the M. persicae gene flow because they showed specific bands according to local strains.