Migrasomes are recently identified vesicular organelles that form on retraction fibers behind migrating cells, cellular contents are released from migrasome by a process named migracytosis. The function of migrasomes in living organisms is unknown. Here we show that migrasomes are formed during zebrafish gastrulation, signaling molecules such as chemokines are enriched in migrasomes. Migrasomes are clustered on spatially restricted area in embryo where they provide regional cues for organ morphogenesis. Our study shown migrasome is signaling organelles which integrate spatial and specific biochemical information to coordinate migrating cells in complex biological processes such as morphogenesis.