The aryl hydrocarbon receptor (AHR) is a ligand-activated transcription factor that dimerizes with ARNT to mediate responses to compounds such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). TCDD and other AHR agonists cause toxic responses in early life stages of fish, including the zebrafish, Danio rerio. The most well characterized target gene for the AHR/aryl hydrocarbon receptor nuclear translocator (ARNT) dimer is a cytochrome P450, CYP1A. Induction of CYP1A by TCDD has been correlated with certain toxic responses in developing zebrafish and has been postulated to mediate these responses. To determine whether CYP1A is the important downstream effector enzyme for the AHR/ARNT pathway, we used morpholino oligonucleotides (MOs) to block induction of CYP1A in response to TCDD in zebrafish embryos. Although the zfcyp1a-MO effectively prevented CYP1A up-regulation, it did not prevent the signs of developmental toxicity, including pericardial edema, slowed blood flow, craniofacial malformation, and defects in erythropoiesis. We conclude that the important target for the AHR/ARNT pathway in developing zebrafish exposed to TCDD is not zfcyp1a. This suggests an alternative model in which TCDD-activated AHR/ARNT disrupts the normal process of growth and development by altering programs of gene expression or function.