Our prior research revealed that there are 2 mitochondrial clades of Aphelinus mali (Haldeman) (Hymenoptera: Aphelinidae) in China, which are known as SD clade and LN clade. To further reveal their genetic characteristics and to determine the degrees of hybridization and gene flow between the 2 clades of A. mali in China, we analyzed the genetic diversities and genetic structures of 16 populations from 6 provinces (Shandong, Liaoning, Hebei, Shanxi, Xinjiang, and Yunnan) using 8 micro satellite loci. Our results showed that among the pure populations in the SD and LN clades, the greatest genetic diversities were found in the Qingdao, Shandong (QD) population and in the Dalian, Liaoning (DL) population. QD was the first population of the SD clade to be established, and DL was the first population of the LN clade to be established. In addition, genetic diversity was not substantially lower - and in some cases it was greater - in mixed-clade populations than in QD and DL. Individuals within each mitochondrial clade could not be differentiated based on microsatellite loci. Our data confirmed that the QD and DL populations, which were the first to be established in China, have served as bridgeheads for the other SD and LN populations in China. The results demonstrated that the hybridization or gene flow has occurred between the 2 mitochondrial clades.