The process of lymphatic vascular development also known as lymphangiogenesis occurs in the embryo from a sub-population of venous endothelial cells that acquire a lymphatic endothelial cell fate. The main molecular switch responsible to drive the transition from venous to lymphatic identity is the transcription factor SOX18. We took advantage of Sox18 mutant mice to perform a micro-array analysis of purified lymphatic endothelial cells from the skin of both wild type and Sox18 heterozygous mutant mice and identified a subset of Sox18-regulated genes with no previously implicated function in lymphangiogenesis. To validate on a large scale top gene candidates (>100) from the micro-array, an expression pattern and morpholino knockdown screen was performed in zebrafish and identified the arap3a gene (ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3) as enriched in zebrafish vasculature throughout embryogenesis. At 56 hours post fertilization (hpf) in zebrafish, we observed that arap3a knock down generates a severe decrease in lymphatic precursor cells and block thoracic duct formation. By contrast, arterial and venous differentiation and sprouting of venous derived intersegmental vessels remained unaffected, demonstrating the specific lymphatic function of arap3a in this model system. In mice, Arap3 is expressed in a polarized fashion in lymphatic endothelial cell precursors in the cardinal vein suggesting a conserved role in lymphangiogenesis. Conditional loss of Arap3 function in endothelial cells triggered severe subcutaneous edema at 14.5 days post coitum (dpc) and skin lymphatic vessels display severe mis-patterning defects whereas the blood vasculature remained unaffected. Finally, we found in fish and in cultured LECs that ARAP3 acts downstream of vascular endothelial growth factor-c (Vegfc) and may be considered an effector of Vegfc/Vegfr3 signaling to modulate lymphatic endothelial cell migration. Our work reveals a major regulator of lymphatic vessel morphogenesis and network assembly downstream of the VEGF-C pathway and provides the molecular basis to further target VEGF-C signaling with the view to blocking lymphatic remodeling during solid tumour metastasis.