Abstract— Several natural materials have been used as traditional medicine for generations to treat various diseases in Indonesia. One of the most widely used plants is Syzygium polyanthum (Wight) Walp. Meanwhile, the in silico toxicity prediction method is a computational approach used to analyze, simulate, visualize, or predict the toxicity of chemicals. It also includes all methodologies for analyzing biochemical properties based on the chemical structure. Identification of compounds using LC-MS/MS and in silico toxicity prediction was carried out via pkCSM ( http://biosig.unimelb.edu.au/pkcsm). The result showed that Syzygium polyanthum contain qoniferin, juncusol, retusine, and quercetine. Furthermore, the toxicity prediction showed that coniferin has a high oral dose toxicity value. Therefore, it is safer to use, does not inhibit CYP1A2, CYP2C9, CYP2D6, and CYP3A4, has hepatotoxic effects, but no toxic AMES.