The olfactory mucosa of the zebrafish consists of 3 morphological types of olfactory receptor neurons (ORNs): ciliated, microvillous, and crypt cells. Previous studies in the zebrafish have revealed differential projections of ciliated and microvillous ORNs, which project to different glomerular fields. However, the bulbar targets of zebrafish crypt cells were not identified. Here, we analyze the relationship between crypt cells of the olfactory epithelium and dorsal glomerular fields of the zebrafish olfactory bulbs, as wells as the connections between these bulbar regions and forebrain regions. For this purpose, a lipophilic carbocyanine tracer (DiI) was used in fixed tissue. Application of DiI to the dorsomedial glomerular field mainly labeled crypt cells in the zebrafish olfactory epithelium. By contrast, application of DiI to the dorsolateral glomerular fields mainly labeled bipolar ORNs and only occasionally crypt cells. Bulbar efferent cells (mitral cells) contacting these dorsal glomerular fields project to different telencephalic areas, with the posterior zone of the dorsal telencephalic area (Dp) as the common target. However, dorsomedial and dorsolateral glomerular fields projected differentially to the ventral telencephalon, the former projecting to the ventrolateral supracommissural region. Retrograde labeling from the ventrolateral supracommissural region revealed mitral cells associated with 2 large glomeruli in the bulbar dorsomedial region, which putatively receives inputs from the crypt cells, indicating the existence of a crypt cell olfactory subsystem with separate projections, in the zebrafish. The comparative significance of the secondary olfactory pathways of zebrafish that convey information from crypt cells is discussed.