While the explosion of genomic data and tools is fully apparent for model organisms, these tools are arguably changing paradigms most quickly in those species for which genetic studies are most challenging. One such species is the honey bee, Apis mellifera. New tools and resources for this species (e.g. [2,17]), an impending genome-sequencing project and new interdisciplinary teams will help bring the unique traits of honey bees into the world of comparative genomics. Several factors make honey bees a compelling choice for genomic studies. First, bees are outstanding experimental subjects for animal behaviour and learning, thanks to a well-known reward system [12], symbolic language [9,16] and phenomenal learning abilities [13]. Honey bees and other social insects also provide extreme examples of developmental switches, or polyphenisms — the generation of distinct phenotypes from an equivalent genetic background [5,6]. Associated with this switch are two traits that pique the interest of medical researchers — fertility and longevity. While workers are nearly sterile, queens lay hundreds of thousands of eggs each year, and live 10–20 times longer than workers. The causes and consequences of the queen–worker split, long known from the standpoint of nutrition, are ripe for genomic analyses.