The eastern honeybee Apis cerana and the western honeybee Apis mellifera are the two most economically valuable honeybee species used in apiculture. In market, the price of Apis cerana honey (ACH) is usually several times higher than that of Apis mellifera honey (AMH) due to the production limit, resulting in wide adulteration and counterfeiting of ACH by AMH. In the present study, we compared honeybee secretions in these two kinds of honey, and found significant differences in protein profiles and hydrocarbon components. The SDS-PAGE pattern showed three species-specific bands with molecular weights between 15.0 and 29.4 KDa in ACH, and six species-specific bands in AMH with molecular weights between 13.8 and 33.1 KDa. The GC-MS-MS detection of the petroleum ether extracts of the two kinds of honey showed that 17-Pentatriacontene and Hentriacontane were the characteristic constituents of ACH and AMH, respectively. These two methods constitute a system to satisfy different needs for entomological authentication of honey samples.