The use of microorganisms in the degradation and detoxification of many toxic xenobiotics, especially pesticides, is an efficient tool for the decontamination of polluted sites in the environment. A novel bacterial strain (M1) was isolated from several water samples contaminated with methomyl which is capable of degrading methomyl pesticide (1000 ppm) in the presence of 0.05% glucose. These water samples were collected from different irrigation sites in Egypt where methomyl is heavily applied. The partial sequence of 16SrRNA gene of the isolate showed the highest similarity to Stenotrophomonas maltophilia. Restriction fragment patterns of isolated plasmid DNA showed that this strain harbours two different plasmids PMa (8Kb) and PMb (5Kb). PMb succeeded to be transferred to Escherichia coli DH5α strain. This transformed strain (M2) acquired the ability to grow in the presence of methomyl (1000 ppm) and 0.05% glucose. So it was deduced that the gene responsible for the degradation process was encoded by this plasmid. The ability of the two strains M1 and M2 to degrade methomyl was detected by using solid phased extraction coupled to capillary liquid chromatography-electrospray ionization-mass spectrometry (SPE-LC-ESI-MS).