The lateral line system (LLS) is a sensory organ present in fishes and in the larval stage of aquatic amphibians, which provides the animal with information about its surrounding environment. Mechanoreceptive sensory cells in the LLS of fishes are grouped into neuromasts that are considered the morphological unit of this system. Structurally the neuromast consists of a central cluster of hair cells with a ring of support cells with some lateral mantle cells. The LLS is localized in both the body surface (superficial neuromast or pit organs) and in a system of canals distributed along the head, trunk and tail (deep neuromast) (Cernuda‐Cernuda et al., 1996). The study of hair cells in the neuromast of fishes is becoming of a great interest, since they are similar in structure and function to the sensory cells of the inner ear and show some identical immunohistochemical properties (Foster et al., 1993). Recently, we have demonstrated the occurrence and the presence of S100 protein in the neuromast hair cells of some teleostean species (Abbate et al., 2002; Germanà et al., 2004). The zebrafish has become an ideal model for the study of developmental genetics, and the neuromast has been used as a model for the study of vertebrate auditory system (Withfield, 2002), so the need for cell selective markers has increased dramatically. Therefore, in this study we have investigated by tissue and whole‐mount immunohistochemistry the presence of S100 protein in both deep and superficial neuromasts in the zebrafish larval, juvenile and adult stages. The results of this work demonstrated that the localization of S100 protein was restricted only to the hair cells of the neuromast at all the examined ages. The mantle cells and supporting cells within the neuromast were unreactive. Nevertheless, heterogeneity has been detected in the S100 protein expression by hair cells, independent of their localization within the neuromast. Our data suggest that the S100 protein is a specific marker for sensory cells in the neuromast of zebrafish at post‐embryonic different stages of development, and it could be important for the analysis of development, regeneration and turnover of hair cells.