Encarsia suzannae is a parasitoid wasp which hosts one of the best characterized systems of cytoplasmic incompatibility (CI) caused by Candidatus Cardinium hertigii. CI occurs when a male E. suzannae infected with Cardinium (strain cEper1) mates with an uninfected female, resulting in high mortality rate of the offspring. In this insect-endosymbiont system, it is not only important to characterize the CI-causing bacteria, but knowing the E. suzannae host expression profile is also vitally important to determine interactions between the two. Furthermore, species in the genus Encarsia are important biocontrol agents as Encarsia parasitizes various plant crop pests. The transcriptome of E. suzannae can therefore also be used in comparison to or as a proxy for other biologically relevant Encarsia species or other parasitoid wasps.