Leptopilina heterotoma is an obligate parasite of Drosophila species. In order to ensure growth and development of offspring, venom proteins and particles are injected during egg laying in the host body. Genomic characterization will allow detailed investigation of this host-parasite model. The genomes of male and female L. heterotoma were sequenced and assembled separately. The N50 for both assemblies is greater than 4,800 bp.