Royal jelly (RJ) is a widely used natural food. It is also a major source of nutrition for queen bees and plays a key role in their development. RJ is secreted from the hypopharyngeal and mandibular glands of young adult worker bees. The regulation of gene expression in these two glands may influence the development of queen bees by affecting the content of RJ. This study investigated the epigenetic effects in these two glands in young adult worker bees treated with histone deacetylase inhibitors (HDACis), a U.S. Food and Drug Administration-approved drug, suberoylanilide hydroxamic acid (SAHA), and NBM-HD-1, a novel compound synthesized in this laboratory. Western blot analyses indicated that the levels of acetyl-histone 3 and p21 protein expression in MCF-7 cells increased markedly after treatment with NBM-HD-1. The data proved that NBM-HD-1 was a novel and potent HDACi. Furthermore, a method of affecting epigenetic regulation of the mrjp family gene in the hypopharyngeal and mandibular glands of young adult worker bees was developed by feeding young adult worker bees HDACi. Epigenetic regulation produced several important biological effects. A marked change in the protein composition of the RJ secreted from these treated bees was found. Only the ratio of specific major royal jelly protein 3 (MRJP3) was significantly altered in the treated bees versus the untreated controls. Other MRJP family proteins did not change. This alteration in the ratio of royal jelly proteins resulted in a significant increase in the body size of queen bee larvae. The data seem to suggest that HDACis may play an important role in the epigenetic regulation of the hypopharyngeal and mandibular glands of young adult worker bees. They appear to change mrjp3 gene expression and alter the ratio of MRJP3 protein in RJ. This study presents the first evidence that HDACis are capable of regulating the ratio of MRJP3 proteins in RJ, which has the potential to change the body size of queen bees during their development.