The strong dimorphism in ovary phenotype seen between honey bee queens and workers represents the anatomical fixation of reproductive division of labor. We review the developmental processes by which the divergent ovary phenotypes become established, mainly focusing on the massive programmed cell death (PCD) that destroys most of the ovariole primordia in the worker ovary during larval development. Ovary-specific transcriptome analyses revealed a set of differentially expressed genes associated with PCD, including two long noncoding RNAs. PCD also plays a major role regulating ovarian activity in adult honey bee workers, and a major effect candidate gene mediating this process is Anarchy, previously identified through classical genetics in a rebel worker strain. Finally, we ask how the strong ovary phenotype dimorphism in the genus Apis may have evolved, and we discuss this by contrasting honey bees with the equally eusocial stingless bees. Through a comparison of their mating systems (polyandry versus monandry), as well as comparative data on female and male gonad structure across several families of bees, we propose the hypothesis that the exceptional gonad structure in Apis queens and drones evolved via shared developmental pathways. Furthermore, we suggest that selection on massive sperm production in Apis drones may have been a driving force leading to this exaggerated gonad morphology.