Background: FGF signaling is a critical pathway regulating cell migration during gastrulation. Results: Inhibition of FGF signaling up-regulates six microRNAs, partially through loss of LIN28B. FGF-regulated microRNAs target proteins important for gastrulation, including serine/threonine and tyrosine kinase receptors. Conclusion: FGF signaling regulates microRNA abundance to control gastrulation. Significance: This identifies a new mechanism by which FGF signaling regulates gene expression.