ABSTRACT The mushroom body (MB) is a uniquely identifiable brain structure present in most arthropods. Functional studies have established its role in learning and memory. Here we describe the early embryonic origin of the four neuroblasts that give rise to the mushroom body and follow its morphogenesis through later embryonic stages. In the late embryo, axons of MB neurons lay down a characteristic pattern of pathways. eyeless (ey) and dachshund (dac) are expressed in the progenitor cells and neurons of the MB in the embryo and larva. In the larval brains of the hypomorphic eyR strain, we find that beside an overall reduction of MB neurons, one MB pathway, the medial lobe, is malformed or missing. Overexpression of eyeless in MBs under the control of an MB-specific promoter results in a converse type of axon pathway abnormality, i.e. malformation or loss of the dorsal lobe. In contrast, loss of dachshund results in deformation of the dorsal lobe, whereas no lobe abnormalities can be detected following dachshund overexpression. These results indicate that ey and dachshund may have a role in axon pathway selection during embryogenesis.