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DNA sequence data from male reproductive genes in numerous taxa have shown that these genes typically evolve more rapidly than other genes, often as a result of directional selection. In the genus Drosophila, the rapidly evolving male accessory gland protein genes (Acps) of melanogaster subgroup flies have contributed to this observation. Acps are small proteins that are transferred to females during mating as a major component of the seminal fluid and are considered agents of chemical communication between the sexes. Acps are known to contribute to normal ovulation and sperm storage, as well as increase oviposition rates and reduce female receptivity. Thus, Acps are considered likely targets of directional selection because of their potential roles in postcopulatory sexual selection and antagonistic coevolution between the sexes. Outside of melanogaster subgroup Acps, little is known about the evolutionary biology of male reproductive genes in Drosophila. For example, the male testis contains a richly diverse transcriptome but no studies have explored the evolutionary dynamics of a large set of testis-expressed genes. If clear differences in the evolutionary dynamics of different classes of male reproductive genes exist, empirical documentation of these differences will help identify the specific evolutionary forces at work. Additionally, mating systems differ between Drosophila species, potentially affecting the evolutionary dynamics of Acps across lineages. Comparative analyses of Acps from species with different mating systems are needed to address this issue. Finally, if Acps are generally rapidly evolving in Drosophila species, comparative analyses of orthology and Acp gene loss/gain are needed to determine how Acps respond to persistent directional selection across lineages. The data presented here aim to address these questions. Included are polymorphism and divergence data from 56 genes of Drosophila arizonae and D. mojavensis, repleta group species with mating systems that differ dramatically from melanogaster subgroup flies. The sample includes 19 Acps, 31 testis-expressed genes, and six more evenly expressed genes. Comparative genomics analyses of D. melanogaster-D. mojavensis male reproductive genes and D. melanogaster-D. pseudoobscura Acps are also presented to address questions of functional conservation across lineages.