Odor molecules are transduced by thousands of olfactory sensory neurons (OSNs) located in the nasal cavity. Each OSN expresses a single functional odorant receptor protein and projects an axon from the sensory epithelia to an olfactory bulb glomerulus, which is selectively innervated by only one or a few OSN types. We used whole-mount immunocytochemistry to study the neurochemistry and anatomical organization of glomeruli in the zebrafish olfactory system. By employing combinations of antibodies against G-protein α subunits, calcium-binding proteins, and general neuronal markers, we selectively labeled various OSN types, their axonal projections to glomeruli, and the detailed anatomical distributions of individual glomeruli in different regions of the olfactory bulb. In this way we identified ≈140 glomeruli in each olfactory bulb of mature zebrafish. A small subset (27) of these glomeruli was unambiguously identifiable in nearly all animals examined. These units were large and, located mainly in the medial olfactory bulbs. Most glomeruli, however, were comparatively small, anatomically indistinguishable, and located in coarsely circumscribed regions; almost all of these latter glomeruli were innervated by OSNs that were labeled with anti-Gα s/olf and/or anti-calretinin antibodies. Collectively, our results provide a uniquely detailed description of a vertebrate olfactory system and highlight anatomically distinct parallel neural pathways that mediate early aspects of olfactory processing in the zebrafish. J. Comp. Neurol. 520:2317–2339, 2012. © 2012 Wiley Periodicals, Inc.