The basic helix-loop-helix (bHLH) transcription factors play important roles in a wide range of developmental processes in higher organisms. bHLH family members have been identified in a dozen of organisms including fruit fly, mouse and human. In this study, we identified 51 bHLH sequences in silico in the honey bee, Apis mellifera L. (Hymenoptera: Apidae), genome. Phylogenetic analyses revealed that they belong to 38 bHLH families with 21, 11, 9, 1, 8 and 1 members in high-order groups A, B, C, D, E and F, respectively. Using phylogenetic analyses, all of the 51 bHLH sequences were assigned to their corresponding families. Genes that encode ASCb, NeuroD, Oligo, Delilah, MyoRb, Figa and Mad were not found in the honey bee genome. The present study provides useful background information for future studies using the honey bee as a model system for insect development.