During early embryonic development, a collection of mechanisms regulate the formation of complex structures by temporally and spatially controlling cell fate decisions. This control is largely mediated by intercellular signaling pathways and secreted molecules. In this dissertation, I studied the molecular mechanisms regulating two important patterning processes, somitogenesis and neurogenesis, during vertebrate development. Somitogenesis is a highly controlled process which segments the mesoderm and outlines the vertebrate body axis. The Notch pathway is vital for the regulation of synchronized gene expression while FGF signaling regulates the ability of presomitic mesoderm to mature and form segment boundaries. It is important to identify the regulators of Notch and FGF signaling to dissect how temporal and spatial cues are established during somitogenesis. Here, I report that the embryonic lethal SBU2 mutation is a result of a nonsense mutation on spt6 gene. These mutants have wide variety of developmental problems including severe somite defects. I found that Spt6 is essential for the Notch pathway regulated transcriptional response and that the somite defects in SBU2 mutants are the result of suppressed Notch signaling. In a complementary study, I investigated the function of ChCh and Sip1a during zebrafish somitogenesis. Microinjection of chch and sip1a morpholinos caused formation of short and narrow somites, suggesting that these genes have indispensable roles in regulating somite formation in zebrafish. Further analysis of chch and sip1a morphants indicated persistent cyclic her1 and her7 expression as well as rostral expansion of fgf8 expression. These results demonstrated novel roles for ChCh and Sip1a in repression of FGF8 activity during somitogenesis. Neural development is another important process which generates and shapes the nervous system. This progression is controlled by both negative and positive regulators. Rest is a transcriptional repressor which silences neural promoters in non-neural cell lines but the function of Rest in early neural development in-vivo is not studied extensively. Here, I studied the function of Rest in zebrafish neurogenesis. Targeted mutation of rest caused de-repression of a subset of Rest target genes during early development and in the long term. Overall, I showed that although Rest is required for regulation of neural genes in-vivo, it is not necessary for early neural development.