The molecular phylogeny of the Subfamily Mesochorinae (Hymenoptera: Ichneumonidae) was inferred from nucleotide sequence variation across a 424-bp region in the Cytochrome b and a 430-bp region in the Cytochrome oxidase I of mitochondrial genome. Both genes indicate strong base bias at the third codon position and AT trans versions occurred more frequently than other type of substitutions. Maximum parsimony and Maximum likelihood analyses based on the CB gene separately give strong support for similar relationships based on morphological data. However, the phylogeny based on COI gene and combined data sets shows relationships discordant with both morphology and Cyt b.