Nanog has been implicated in establishment of pluripotency in mammals and in zygotic genome activation in zebrafish. In this study, we characterize the development of MZ (maternal and zygotic null) mutant zebrafish embryos Without functional Nanog, epiboly is severely affected, embryo axes do not form and massive cell death starts at the end of gastrulation. We show that three independent defects in MZ mutants contribute to epiboly failure: yolk microtubule organization required for epiboly is abnormal, maternal mRNA fails to degrade owing to the absence of miR-430, and actin structure of the yolk syncytial layer does not form properly. We further demonstrate that the cell death in MZ embryos is cell-autonomous. Nanog is necessary for correct spatial expression of the ventral-specifying genes , and , and the neural transcription factor It is also required for the correctly timed activation of endoderm genes and for the degradation of maternal mRNA via miR-430 Our findings suggest that maternal Nanog coordinates several gene regulatory networks that shape the embryo during gastrulation.