In the present study, a detailed amino acid analysis based on Ultra Performance Liquid Chromatography (UPLCTM) was performed. The results showed significant increase in arginine, proline and glutamine amounts in syncytia. Ammonium ions were also increased as an important precursor in arginine, proline and glutamine biosynthesis. In addition, branched chain amino acids and amino acids of shikimic acid based pathway were also enriched in syncytia. This study opens a door to understand the remodeling of amino acid metabolism in response to H. schachtii infection in plants.