Female reproductive tract secretions are putatively involved in a diverse array of reproductive events, including sperm storage and survival, ejaculate-female interactions, ovulation, postmating immune response, lubrication for egg-laying, and the production of protective egg coating. However, little is known about the source, contents or function of these secretions. We characterized mating-induced gene expression in the parovaria, a secretory gland of the female reproductive tract, using RNAseq analysis at 3 time points (premating, 6hrs, and 24hrs postmating). Genes significantly upregulated postmating included proteases, peptidases and anti-microbial genes, thereby supporting established functions of female secretions in seminal fluid processing and postmating immune response. Many of these genes have similar postmating expression patterns in other female reproductive structures, indicating a suite of redundant functions spatially distributed throughout the female reproductive tract. We also identified genes with distinct expression patterns in the parovaria, suggesting unique functions of these glands. In particular, we found an enrichment of highly expressed genes on the X chromosome, including several novel genes created through gene duplication occurring during the radiation of the melanogaster subgroup. Contributions of these genes to postmating changes in female physiology and fertility are currently being assessed using an RNAi knockdown approach.