Apolipoproteins, the major components of lipoproteins, play physiological roles in lipoprotein metabolism. Contrary to the well-documented effects on plasma lipid, little is known about the function and regulation of Apolipoproteins during embryonic development. Here we have shown that apolipoprotein C1 (apoc1) gene is highly expressed in the yolk syncytial layer, a structure implicated in embryonic and larval nutrition. The apoc1 transcripts are also observed in the deep cell layer at the ventral and lateral region during gastrulation, and in the tail paraxial mesoderm during somitogenesis. By whole-mount in situ hybridization and quantified RT-RCR, we further demonstrate that apoc1 expression is induced by bone morphogenetic proteins (BMPs) signaling, while retinoic acid (RA) signaling suppresses the expression of BMP ligands and inhibits the BMP effect in this process.