In the zebrafish olfactory epithelium, three morphologically distinct olfactory neurons express different marker proteins. We utilize this feature to access developmental dynamics of one of the neuron types, the crypt cells, to determine whether they are differentiated at a stage similar to other olfactory neurons. Immunohistochemical studies using an S100 antibody that specifically recognizes crypt cells showed that S100-positive cells appear in olfactory rosettes as early as at 2day postfertilization (dpf). However, some of the rosettes did not have any S100-positive cells until 4 dpf. The number of S100-positive cells in individual rosettes increased steadily over the next 3days before it decreased significantly. There were 7.8 S100-positive cells per rosettes on average in larvae at 7 dpf. The number reduced to 2.2 at 9 dpf. A recovery to a pre-reduction level was detected in 12 dpf larvae. We also observed S100-positive cells in neuromasts of the lateral line system in 2 dpf larvae, suggesting that the crypt cells and sensory cells in the neuromasts have similar onsets of differentiation. Our data have provided a time line of differentiation of crypt cells in development of the olfactory system and demonstrated that this type of cell is differentiated at a stage similar to ciliated and microvillous olfactory neurons. A nonlinear growth trajectory of the crypt cell population in the first nine days of zebrafish development implicates a possible functional significance of crypt cells in early life stages of zebrafish.