The central complex (CX) in the brain of insects is a highly conserved group of midlinespanning neuropils consisting of the upper and lower division of the central body, the protocerebral bridge, and the paired noduli. These neuropils are the substrate for a number of behaviors, most prominently goal-oriented locomotion. Honeybees have been a model organism for sky-compass orientation for more than 70 years, but there is still very limited knowledge about the structure and function of their CX. To advance and facilitate research on this brain area, we created a high-resolution threedimensional atlas of the honeybee's CX and associated neuropils, including the posterior optic tubercles, the bulbs, and the anterior optic tubercles. To this end, we developed a modified version of the iterative shape averaging technique, which allowed us to achieve high volumetric accuracy of the neuropil models. For a finer definition of spatial locations within the central body, we defined layers based on immunostaining against the neuropeptides locustatachykinin, FMRFamide, gastrin/cholecystokinin, and allatostatin and included them into the atlas by elastic registration. Our honeybee CX atlas provides a platform for future neuroanatomical work.