Accessory gland proteins (ACPs) of Drosophila represent a group of proteins that are transmitted to females during mating; and, therefore, influence reproductive success through changes in female behavior, physiology, and sperm utilization. Additionally, ACPs are known to undergo rapid evolutionary changes that are thought to be due to important roles they play in reproductive success during mating. However, the reproductive advantage of ACPs in one species, do not necessarily convey an advantage in other species. Two such ACPs are Sfp79B (Seminal fluid protein 79B) and msopa (male specific opa containing gene). Both of these genes are highly expressed, specifically in the accessory glands of D. melanogaster. Additionally, Sfp79B peptides from males have previously been detected in the lower reproductive tracts of mated female in both D. melanogaster and D. simulans, but not in D. yakuba. In this study the two ACP encoding genes Sfp79B and msopa were annotated on the 3L chromosomal arm of D. elegans between the RpLP0 and olf413 homologues as part of the Genomics Education Partnership (GEP). To better understand the evolution of these genes, a survey of 19 species in the subgenus Sophophora were analyzed, including 16 from the melanogaster group and 3 from the obscura group. Both have not always been detected during previous annotations, which is likely due to their small size. Therefore, the genomic regions between the RpLP0 and olf413 homologues were analyzed for the presence of these genes in different species. Of these 19 species, Sfp79B was present in 13 of the species, but was absent in some members of the melanogaster, suzukii, and takahashii subgroups. Furthermore, in both ananassae and pseudoobscura subgroups, duplications of Sfp79B were detected. While msopa is present in both the melanogaster and obscura group, it was not detected in the ananassae subgroup. Additionally, in some of the groups msopa was found to be under positive selection based on Ka/Ks values. Future analysis of RNA expression will be conducted to verify whether these annotated gene products of Sfp79B and msopa are produced in select representative species. Together, this data demonstrates while Sfp79B is absent from some species of Drosophila, it has a larger role in the Sophophora subgenus than originally recognized. Moreover, analysis of both Spf79B and msopa demonstrate that while ACP encoding genes can be found throughout the Sophophora subgenus, rapid evolutionary changes in these genes occur in reproductive pockets.