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Minute parasitoid wasps in the genus Encarsia are commonly used as biological pest control agents of whiteflies and armored scale insects in greenhouses or in the field. They are also a key host of the bacterial endosymbiont Cardinium hertigii which can cause a suite of reproductive manipulation phenotypes, including parthenogenesis, feminization, and cytoplasmic incompatibility; the last being most thoroughly studied in Encarsia suzannae. Despite their biological and economic importance, there are currently no published Encarsia genomes and only one public transcriptome. In this study, we applied a mapping-and-removal approach to eliminate known contaminants from previously-obtained Illumina sequencing data. We generated de novo transcriptome assemblies for both female and male E. suzannae which contain 45,986 and 54,762 final coding sequences, respectively. Benchmarking Single-Copy Orthologs (BUSCO) results indicate both assemblies are highly complete. Preliminary analyses revealed the presence of homologs of sex-determination genes characterized in other insects and putative venom proteins. These transcriptomes will be valuable tools to better understand the biology of Encarsia wasps and their evolutionary relatives. Furthermore, the separate male and female assemblies will be particularly useful references for studies involving insects of only one sex.