Many organisms encounter and overcome extreme condition which is not ideal for embryo development by diapause, a unique surviving approach by which embryos put all developmental processes in temporary arrest to live through an adverse environment. Although similar dormancies are widely observed among species, still little is understood about the underlying mechanical principles of diapause. It is especially intriguing that how distinct tissues and cells in different developmental programs can altogether be suspended at the same time, and if their developmental status/identity are maintained or modified during the ‘suspended state’ of diapause. Zebrafish is known to suspend its early embryo development when oxygen is deprived, but only for a short period of time (up to 24 hours). A similar but more significant case of diapause can be found in turquoise killifish Nothobranchius furzeri, which possess an ability to suspend embryonic development at the end of somitogenesis. Living in ephemeral ponds where water presents only during the brief annual rain seasons, newly laid killifish embryos prepare the coming drought by entering diapause for months, sometimes even years, until the ponds are refilled with water again in another rain season. This lengthy diapause in killifish is obligatory and can still occurs in lab conditions, providing a unique opportunity to study early embryo development and their crosstalk with diapause. Our transcriptome profiling revealed a dramatic shift of gene expression patterns at the transition between embryogenesis and diapause. Immediately after diapause entry, more than 35% of genes changed their expression levels for over 2 folds, indicating that diapause embryos were switching into a phase distinct to embryogenesis. With many antagonistic mechanisms upregulated, various embryonic developmental programs were either put on hold or erased in diapause. Key regulators of cell differentiation such as NeuroD1, and MyoD1 were heavily downregulated, and critical morphogens of embryogenesis such as Wnt and Fgf were mostly depleted. Interestingly, with developmental processes suspended in diapause, many general or tissue-specific genes related to stress tolerance, protection and homeostasis were highly expressed for already developed tissues, especially neural tube/crest and muscles. Overall, diapause provides a unique pausing point to further dissect and understand the developmental programs and their signaling pathways in early embryo development. The research in embryonic diapause not only provides insights of tissue and cell homeostasis during embryo development, but also a complementary platform for various known or ongoing zebrafish studies in early embryo developments.