Psychophysical studies indicate that structural features of odorants differentially influence their perceived odor. In the olfactory bulb (OB), odorants are represented by ensembles of activated glomeruli. Here we used optical imaging of intrinsic signals to examine how these structural features are represented spatially in the sensory map of the rat OB. We found that the dorsal OB contained two topographically fixed domains; constituent glomeruli in each domain could be activated by odorants with particular functional groups. Within each domain, other structural features such as carbon chain length and branching were represented by local differences in patterns. These results suggest that structural features are categorized into two classes, primary features (functional groups) that characterize each domain, and secondary features that are represented by local positions within each domain. Such hierarchical representations of different structural features correlate well with psychophysical structure-odor relationships.