2-Amino-4,6-dimethoxypyrimidine is identified as degradation product of sulfosulphuron in agricultural soil by ESI LC-MS/MS analysis. It was isolated as metabolite during the biodegradation of bensulphuron-methyl by Penicillium pinophilum by liquid chromatography-mass spectrometry. The FTIR and FT-Raman spectra of 2-amino-4,6-dimethoxypyrimidine has been reported. Hydrogen bonding in the molecules of 2-amino-4,6-di-methoxy-pyrimidine has been investigated.