Topographic maps are a fundamental feature of neural networks in the nervous system. Understanding the molecular mechanisms by which topographically ordered neuronal connections are established during development has long been a major challenge in developmental neurobiology. The retinotectal projection of lower vertebrates including birds has been used as a readily accessible model system. In this projection, the temporal (posterior) retina is connected to the rostral (anterior) part of the contralateral optic tectum, the nasal (anterior) retina to the caudal (posterior) tectum, and likewise the dorsal and ventral retina to the ventral (lateral) and dorsal (medial) tectum, respectively. Thus, images received by the retina are precisely projected onto the tectum in a reversed manner. For the formation of topographic maps, molecular gradients in origin and targets are essential. To search for topographic molecules in the embryonic retina, we performed a large-scale screening and successfully identified a variety of molecules with various asymmetrical expression patterns along both axes in the developing retina. Included were many novel molecules with unknown functions, together with known molecules. Through analyses of these molecules, we can now present gene cascades for the retinal patterning and for the establishment of topographic retinotectal projection. In addition, we identified protein tyrosine phosphatase receptor type O (Ptpro) as a specific PTP that regulates Eph receptors. We show that Ptpro controls the sensitivity of retinal axons to ephrins, and thereby plays crucial roles in the topographic projection.