Abstract: 【Objective】The objective of this study is to compare the proteome and phosphoproteomic during the three days development of Apis cerana cerana and A. mellifera ligustica, investigate the characteristics of embryonic development and gain an in-depth understanding of the developmental biology of the drone embryos, and to lay a foundation for the future genetic improvement of honeybees.【Method】Two-dimensional gel electrophoresis (2-DE) was employed to compare the proteomic and phosphoproteomic differences between the drone embryogenesis of the two bee species at three time-points of 24, 48 and 72 h, respectively. The level of protein expression, pI and molecular weight were determined. Furthermore, some of the differentially expressed proteins were analyzed by mass spectrometry and bioinformatics.【Result】In total proteome, 332, 362 and 340 protein spots were detected in drone embryos of A. cerana cerana from day 1 to day 3. Of these, 111, 117 and 112 proteins were phosphorylated, respectively. In the drone embryos of A. mellifera ligustica, 302, 331 and 311 proteins were detected, in which 107, 110 and 106 proteins were phosphorylated. Meanwhile, 214, 239 and 220 proteins were commonly expressed during the first three days of drone embryonic development. Thirty differentially expressed proteins were involved in carbohydrate metabolism and energy production, protein folding, development, regulatory proteins and cytoskeletal proteins.【Conclusion】A larger number of proteins and phosphoproteins were expressed in A. cerana cerana than those in A. mellifera ligustica during the drone embryogenesis, indicating A. cerana cerana needs more protein to regulate its drone embryonic development. About 1/3 protein phosphorylated in both honeybee embryos might be associated with signal transduction, cell proliferation and differentiation during drone embryogenesis. Embryos of A. mellifera ligustica expressed higher proportion of housekeeping proteins than in A. cerana cerana suggest the embryogenesis of A. mellifera ligustica has shaped more conservative manner of development due to its longer evolution history. Function analysis indicates that in the long-term evolutionary process has shaped the two honeybee species perusing their own embryonic development ways to fit their biological characteristics. Some of the important biological characteristics, such as A. cerana cerana is good at collecting sporadic nectar and pollen and defending wasps, and A. mellifera ligustica has higher production of honey and royal jelly, have been partially unraveled by this proteome dataset.