Prox1 is a master regulator for the development of lymphatic vasculature and the induction of lymphangiogenesis. In this study, we identified Prox1 as a new target for small ubiquitin-like modifier 1 (SUMO-1). Lysine 556 (K556) was found to be the major sumoylation site for Prox1 in vitro and in vivo. Mutation of this site (from lysine to arginine K556R) reduced DNA binding and the transcriptional activity of Prox1. Overexpression of Prox1 in EA.hy926 endothelial cells induced expression of lymphatic endothelial cell-specific genes including vascular endothelial growth factor receptor 3 (VEGFR3), fibroblast growth factor receptor 3 (FGFR3) and p57 while expression of K556R mutant Prox1 had little effect. The induction of VEGFR3 by Prox1 in EA.hy926 endothelial cells was an indication of their response to VEGF-C-induced lymphangiogenic signals, including the enhancement of proliferation, sprouting and tube formation and the inhibition of apoptosis. This effect is SUMO-dependent because ectopic expression of SUMO-specific protease 2 (SENP2) effectively reduced Prox1 sumoylation and Prox1-induced VEGFR3 expression. In addition, K556R mutant Prox1 could not induce lymphatic phenotypes. Taken together, our results indicate that Prox1 is a target for SUMO-1 and suggest that sumoylation of Prox1 controls its ability to induce VEGFR3 expression and lymphatic phenotypes in endothelial cells.