AbstractThe central complex (CX) is a defined set of neuropils located on the midline of the protocerebrum in several arthropods and has been implicated in a number of behaviors. To investigate the function of the CX further it is imperative to know the neuroarchitecture of this structure and to ensure all known neuron types conform to a common nomenclature system. Several types of CX neuron have been identified but it is not known if these exist singly or as components of isomorphic sets. We used an enhancer trap approach to study the adult structure, connectivity, and polarity of CX neurons in Drosophila. We observed several isomorphic sets of small‐field neurons including pontine and fb‐eb neurons, and also isomorphic sets of large‐field neurons including R neurons and F neurons. We found that several types of large‐field F neurons existed in isomorphic sets of approximately eight (four per hemisphere) and found evidence for small‐field neuron types existing as isomorphic sets of 16. Small‐field neurons were observed in clearly organized layers. This study provides a novel insight into CX structure and connectivity and provides a set of characterized enhancer trap lines that will be valuable for future study. J. Comp. Neurol. 518:1500–1524, 2010. © 2009 Wiley‐Liss, Inc.