European honeybee (Apis mellifera L.) is a social insect and the colony members exhibit highly advanced social behaviors. The molecular and neural bases that underlie their social behaviors, however, remain largely unclear. The brain of the honeybee show characteristic features in its structure such as well-developed mushroom bodies (MB, higher center in insect brains) and direct neural connection between the MB and optic lobes (OL). Therefore, analysis of the functional differences among brain regions could give important insights into the neural and molecular bases of the honeybee social behaviors. Recently, honeybee genome project has been completed and the proteomic analysis becomes effective technique in the honeybee biology. In the present study, we compared protein expression patterns in the MBs and OLs of the worker brains using two-dimensional gel electrophoresis and identified five and three spots that are detected selectively in the MBs or OLs, respectively. Combination of liquid chromatography tandem mass spectrometry and the database search identified one of the MB-selective spots as cAMP-dependent protein kinase type II regulatory chain, which is consistent with the previous report [1]. The other MB-selective spot was identified as juvenile hormone diol kinase (JHDK) that is also homologous to calexcitin in Cephalopoda, suggesting possible involvement of JH in regulating MB function. In situ hybridization revealed that jhdk is expressed predominantly in a subset of MB interneurons in the worker brain. Furthermore, one of the OL-selective spots was identified as glyceraldehyde-3-phosphate dehydrogenase (G3PDH). In situ hybridization revealed that g3pdh is expressed in broad brain regions including the OLs but not in the MBs. These results indicate that the honeybee brain regions can be characterized by their unique gene/protein expression patterns.