Hybrid sterility studies have typically focused on hybrid males that lack the ability to produce functional gametes; however, considerable variation in fertility exists for hybrid females. Using whole genome microarrays, expression profiles for D. simulans/D. melanogaster hybrid females exhibiting different levels of oogenic development were examined. Hybrid females with higher levels of oogenic development have fewer loci over- or under-expressed compared to pure species expression. These hybrid females also have more loci dominantly expressed like D. melanogaster, especially female reproductive loci and transcription factors. Higher D. melanogaster dominance could be the result of master regulatory switches that act to reduce the regulatory conflict that has accumulated as the species have diverged. One candidate regulatory locus is Hybrid male rescue (Hmr). Hmr interacts with Lethal hybid rescue (Lhr) due to complementary binding domains, and both regulate gene expression in heterochromatic regions. D.melanogaster-like expression of Hmr, Lhr, and out at first (oaf), a female reproductive locus with multiple splice variants, begins in the pupae for the more fertile female hybrids. The hybrid with the highest oogenic development was from the only D. simulans line to express Hmr and all of the oaf variants like D. melanogaster in the pupae. Additionally, reduced inviaibilty rescue was seen with over-expression of oaf in the larval stage and adult expression of Hmr like D. melanogaster and Lhr like D. simulans, consistent with the Dobzhansky-Muller model. Matching expression patterns seem to reduce regulatory conflict and also influence a hybrid's mate choice, as increased preference for mating with D. simulans males was seen with female hybrids expressing two pheromone loci, olfactory-specific C and odorant-binding protein 56h, like D. simulans. These results suggest that reduction in regulatory conflict leads to more reproductive compatibility and hence more fertile hybrid females, and that mate preference is stronger when the loci involved in mating are expressed like the mate chosen.