NQO1, NAD(P)H: quinone oxidoreductase 1, was first identified in rat and its role has been extensively studied. Even the roles of NQO1 in the maintenance of physiological function and disease were largely addressed, whether the tissue specific functions of the NQO1 in organ development remains unknown. In the current study, we identified two NQO1 isoforms (isoform 1 and isoform 2) and examined the expression of nqo1 variants in adult zebrafish organs and embryos at different stages. In adult organs, RT-PCR result indicated that nqo1 variant 1 was mainly expressed in stomach and intestine, while nqo1 variant 2 was expressed in all organs investigated except for heart. Further, RT-PCR result showed that the nqo1 variant 1 and variant 2 were expressed at all the embryonic stages, but nqo1 variant 1 expression level was much lower than that of nqo1 variant 2. To specifically examine the expression pattern of these two different nqo1 variants, we did whole mount in situ hybridization and the results demonstrated that, both of them were maternally expressed at 8-cell stage, and they were all expressed ubiquitously at early stage. At 24 hpf, nqo1 variant 2 was mainly expressed in yolk cells, and slightly in head and eyes. At 48 hpf, nqo1 variant 2 was restricted in lateral line neuromasts. From 72 hpf to 144 hpf, nqo1 variant 2 was mainly restricted in branchial arch, liver, swimming bladder and lateral line neuromasts, while from 124 hpf to 192 hpf, nqo1 variant 2 only restricted in liver, and disappeared in lateral line neuromasts. On the contrary, at the late embryonic stage, nqo1 variant 1 was only expressed in liver and swimming bladder while not in branchial arch and lateral line neuromasts. In conclusion, we systematically analyzed the expression pattern of nqo1 variant 1 and variant 2 in zebrafish at different embryonic stages, and our data implied the possible role of nqo1 in regulating liver, branchial arch and lateral neuromasts development.