Aphelinus mali (Haldeman) (Hymenoptera: Aphelinidae) is an important specific endoparasitoid of Eriosoma lanigerum (Hausmann) (Hymenoptera: Aphididae) with high natural parasitism in the field. By studying the COI gene of the A. mali mitochondrion, two distinct clades, Shandong and Liaoning clades, were found in China. In this paper, the mitochondrial genome of A. mali populations from Shandong province was sequenced and analyzed. In total, 14415 bp were sequenced, representing 93.5% of the total length of the A. mali mitochondrial genome, with six tRNA, trnY, trnM, trnI, trnQ, trnW, trnS1, not sequenced. The unmeasured area was located in an A+T-rich region of approximately 1000 bp. The AT content in the A+T-rich region was as high as 91.3% and this may be why this region has not been detected until now. The A+T content was 84.4% in the measured region, which is higher than that of other Hymenoptera. The AT skew was 0.1291, the highest AT skew known among Hymenoptera, which might be related to the higher AT content of protein-coding genes, rRNA and RSCU AT content. Transport genes (tRNA) had a secondary clover shaped structure, compared with other Hymenoptera; there is a more incomplete secondary structure, and less base mismatch. The mitochondrial genome of A. mali showed considerable rearrangement when compared with the mitochondrial genome of the most primitive arrangement, mainly concentrated in six tRNA genes and the gene region from cob to trnE and from trnL to nad1. The mitochondrial genome of A. mali is quite different from that of other Hymenoptera as can be demonstrated by constructing a phylogenetic tree. This paper provides a basis for further study of phylogeny, genetic structure, and hybridization of A. mali populations.