Parasitoid wasps play a fundamental role in the biological control of pests. However, their morphological identification may be limited due to their small size and the high morphological similarity between species. Our objective was to identify specific genomic variants of the target species Palmistichus elaeisis Delvare & LaSalle, 1993, Tetrastichus howardi (Olliff, 1893), Trichospilus diatraeae Cherian & Margabandhu, 1942, and Trichogramma pretiosum Riley, 1879, (Hymenoptera: Chalcidoidea) by whole-genomic sequencing. Parasitoids were collected from their hosts and established in the laboratory after adult emergence. A sample of each parasitoid was sent to the Departamento de Ciências Biológicas at Universidade Federal do Espírito Santo (UFES) and “Oscar Monte” Entomophagous Insect Collection for morphological identification. Subsequently, samples composed of 20 individuals were preserved in absolute ethanol for DNA extraction. The DNA was extracted, quantified and sequenced on the Illumina Novaseq 6000 platform. Bioinformatic tools were used for quality control, detection of specific genomic variants, principal component analysis (PCA), and support vector machine (SVM). Genomic sequencing generated high-quality data for the analyzed parasitoids, allowing the identification of four specific variants for P. elaeisis, two for Te. howardi, four for Ts. diatraeae and five for Tg. pretiosum. These results provide a precise molecular tool for distinguishing parasitoids used in biological control programs.