Embryonic development is particularly vulnerable to stress and DNA damage, as mutations can accumulate through cell proliferation in a wide number of cells and organs. However, the biological effects of chronic exposure to ionising radiation (IR) at low and moderate dose rates (< 6 mGy/h) remain largely controversial, raising concerns for environmental protection. We employed a systems biology approach involving, transcriptomics and epigenetics to understand how exposures to low to moderate dose rates of IR impact embryonic development, using zebrafish as a model. Our data highlight that the transcriptional program regulating morphogenesis in gastrulating embryos was modified at dose rates greater than or equal to 0.5 mGy/h, which might predict potential neurogenesis and somitogenesis defects observed at similar dose rates later in development. In particular we observed that the retinoic acid pathway was impaired during gastrulation and after organogenesis, and might thus constitute a key event in the progression of the adverse outcomes induced by RI. Future studies will employ functional studies to better characterize the implication of the retinoic acid pathway.