The ubiquity of pathogens in the natural world poses a strong selection force on the evolution of Drosophila immunity. Under the pressure of this natural selection by pathogenic organisms, species diverge along the evolutionary path and depart in phenotypes. Interspecific differences in gene expression are an important contributor to this divergence where gene expression is regulated by both cis-regulatory elements, which affect nearby gene expression levels in an allele-specific fashion, and trans-regulatory elements, which affect gene expression by interacting with linked cis-elements. The relative contributions of cis- and trans-divergence can be estimated by comparing gene expression between two species and allele-specific expression within their F1 hybrids. The total interspecific divergence and the cis-divergence are captured respectively between the parents and within the hybrids, and the trans-divergence is attained by subtracting the cis from the total divergence. We investigated the transcriptional response of Drosophila simulans and D. sechellia to parasitoid wasp infection. Many genes had large expression differences between the two species from cis-regulatory divergence in uninfected and infected conditions alike. However, the divergence of immune response is overwhelmingly driven by trans, suggesting that altering trans-regulatory elements, such as signalling pathways or immune modulators, may allow natural selection to alter the expression of large numbers of immune-responsive genes in a coordinated fashion. I then investigated the transcriptional differences between D. melanogaster and D. simulans responding to injuries and found that constitutive expression divergence between the two species was mostly cis-driven, and there was extensive misexpression of immune-related genes in hybrids.