The lipid mediator sphingosine-1-phosphate (S1P) is a regulator of cardiac development in zebrafish, as disruption of its receptor s1pr2 or transporter spns2 causes migration defects in cardiac progenitors. To examine the genetic interaction of S1P signaling and the cell adhesion molecule fibronectin, we have established a fn;spns2 double mutant. Cardiac migration defects in fn;spns2 mutants were more severe than those in fn or spns2 mutants. We further found that the lower jaw morphology was disorganized in the fn;spns2 mutant, while it had a slightly shortened anterior–posterior distance in the ventral pharyngeal arch in fn and spns2 mutants relative to wild type. Knockdown of fn in the s1pr2 mutant, but not in the s1pr1 mutant, resulted in severe defects in cardiac migration and ventral pharyngeal arch arrangement. Further, in the background of the fn mutant, knockdown of endothelin receptor A (ednra), which was downregulated in the spns2 mutant, caused pharyngeal defects resembling those in the fn;spns2 mutant. These results strongly suggest that Spns2-S1PR2 signaling and fibronectin cooperatively regulate both cardiac and lower jaw development in zebrafish.