Trichopoda pennipesis a tachinid parasitoid of several significant heteropteran agricultural pests, including the southern green stink bug,Nezara viridula, and leaf-footed bug,Leptoglossus phyllopus. To be used successfully as a biological control agent, the fly must selectively parasitize the target host species. Differences in the host preference ofT. pennipeswere assessed by assembling the nuclear and mitochondrial genomes of 38 flies reared from field-collectedN. viridulaandL. phyllopus. High-quality de novo draft genomes ofT. pennipeswere assembled using long-read sequencing. The assembly totaled 672 MB distributed among 561 contigs, having an N50 of 11.9 MB and a GC of 31.7%, with the longest contig at 28 MB. The genome was assessed for completeness using BUSCO in the Insecta dataset, resulting in a score of 99.4%, and 97.4% of the genes were single copy-loci. The mitochondrial genomes of the 38T. pennipesflies were sequenced and compared to identify possible host-determined sibling species. The assembled circular genomes ranged from 15,345 bp to 16,390 bp and encode 22 tRNAs, two rRNAs, and 13 protein-coding genes (PCGs). There were no differences in the architecture of these genomes. Phylogenetic analyses using sequence information from 13 PCGs and the two rRNAs individually or as a combined dataset resolved the parasitoids into two distinct lineages:T. pennipesthat parasitized bothN. viridulaandL. phyllopus, and others that parasitized onlyL. phyllopus.