In this paper, the genetic relationships among six fruit fly species of Bactrocera in Yunnan Province of Southwest China, i.e., B. tau, B. scutellaris, B. scutellata, B. cucurbitae, B. dorsalis and B. correcta, were studied by using the technique of random amplified polymorphic DNA (RAPD). Five primers with good repetition and high polymorphism were screened from 131 primers, and a total of 302 bands were amplified, among which, 111 bands were of genetic polymorphism. The primers OPC-01, OPI-17, OPL-07, OPL-08 and OPL-16 could be used for the identification of the 6 fruit fly species.