The estrogen receptor (ER) genes encode a group of nuclear enhancer proteins, which are important ligand-activated transcription factors, modulating estrogen-target gene transcription. In this study we analyzed expression patterns of three zebrafish ER genes, esr1, esr2a, and esr2b, during development using whole-mount in situ hybridization. High levels of esr2a and esr2b of maternal origin are inherited and segregated to the blastomers. After the mid-blastula transition, the three genes exhibit similar spatio-temporal patterns of expression. In 24 h postfertilization (hpf) embryos, high levels of esr2a and esr2b and low levels of esr1 mRNAs are detected in the epidermis, pectoral fin buds, hatching gland and, to a lesser extent, developing brain. From 24 hpf onward, the expression of the three genes is down-regulated in the epidermis. By 60 hpf, esr2a mRNA is abundant in mature primary neuromasts of the anterior line system and by 3 days postfertilization (dpf), all mature primary neuromasts in both the anterior and posterior lateral line systems express significant levels of esr2a and esr2b transcripts. Histological sections show a high level of esr2a transcripts in both mechanoreceptive hair cells and supporting cells. The transcripts are still detected after neomycin-induced hair cell death, consistent with the presence of esr2a transcripts in supporting cells. From 6 dpf onward, esr2a and esr2b transcripts are robustly co-expressed in primary neuromasts, branchial arches, pectoral fins, and anal papilla, while slight labeling is observed for esr1 transcripts.