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In Hymenoptera, the monophyly of Evaniomorpha has been the focus of debate among different scholars. In this study, we sequenced two mitochondrial genomes of <i>Dendrocerus</i> (Hymenoptera: Megaspilidae) to analyze the mitochondrial genomic features of <i>Dendrocerus</i> and provide new molecular data for phylogenetic studies of Evaniomorpha. The mitogenome sizes of <i>D. bellus</i> and <i>D. anisodontus</i> were 15,445 bp and 15,373 bp, respectively, with the <i>trnG</i> of <i>D. bellus</i> missing. The nucleotide composition was significantly biased toward adenine and thymine, with A + T contents of 81.2% (<i>D. bellus</i>) and 82.4% (<i>D. anisodontus</i>). Using <i>Ceraphron</i> sp. (Ceraphronidae) as reference, the Ka/Ks values of <i>NAD4L</i> and <i>NAD6</i> in <i>D. anisodontus</i> were both greater than one, indicating that non-synonymous mutations are favored by Darwinian selection, which is rare in other hymenopteran species. Compared with <i>Ceraphon</i> sp. gene order, nine operations were identified in <i>D. anisodontus</i>, including four reversals, four TDRLs (tandem duplication random losses) and one transposition, or four reversals and five TDRLs. Phylogenetic analysis of 40 mitochondrial genomes showed that Evaniomorpha was not a monophyletic group, which was also supported by the PBD values. Ceraphronoidea is a monophyletic group and is a sister to Aulacidae + Gasteruptiidae. Based on the conserved region of the newly sequenced mitochondrial genomes, a pair of specific primers MegaF/MegaR was designed for sequencing the <i>COX1</i> genes in Megaspilidae and a 60% rate of success was achieved in the genus <i>Dendrocerus</i>.