The cDNAs encoding the zebrafish homologs of retinoic acid receptor alpha(zRAR alpha) and gamma (zRAR gamma) were isolated and their expression studied in normal and retinoic acid (RA) treated embryos. Expression boundaries in the central nervous system are clearly different from those observed in the mouse, which can only partly be explained by morphogenetic differences. Treatment of embryos with RA induces ectopic zRAR gamma expression in anterior brain structures and both zRAR alpha and zRAR gamma expression in the eyes. Furthermore, striking differences occur in the zRAR gamma expression pattern in pharyngeal arch mesenchyme. Since the development of all of these structures has been shown to be affected by exogenous RA, our data suggest a role for zRAR alpha and zRAR gamma in the establishment of the RA phenotype in zebrafish.