Semaphorin 3A (Sema3A) repels growing olfactory axons that express neuropilin-1 (NP-1), a receptor for Sema3A. The Sema3A-mediated axon guidance seems to be essential for the formation of the glomerular sensory map in the olfactory bulb (OB). To understand whether and how Sema3A is involved in sensory map formation, we examined the glomerular map in the OB of adult Sema3A-deficient mice. In wild-type mice, NP-1-positive glomeruli form the lateral and medial bands and avoid the anteromedial and ventral regions of the OB. In the Sema3A-deficient OB, NP-1-positive glomeruli spread over the entire OB, and we consistently found the ectopic arrangement of NP-1-positive glomeruli in the anteromedial and ventral regions. In addition, a specific subset of NP-1-negative and olfactory cell adhesion molecule-positive glomeruli, especially those in the anteromedial region, disappeared from the mutant OB. These results show a critical role for Sema3A in the spatial arrangement of glomeruli in the OB. Optical imaging from the dorsal OB showed that the distorted glomerular map conserved molecular-feature domains. However, the positions of the domains were shifted, which suggests a secondary rearrangement of the glomerular map in the Sema3A-deficient OB.