The Pseudomonas fluorescens isolate FP 7 was found to protect the tomato plants against soil borne fungus, Pythium aphanidermatum. The ability to induce defense proteins viz. -1,3 glucanase, peroxidase (PO), polyphenol oxidase (PPO) and phenylalanine ammonia lyase (PAL) by this P. fluorescens isolate FP 7 against P. aphanidermatum fungus was further studied. Increased activity of PO, PPO and -1,3 glucanase were observed in plants pretreated with FP 7 isolate. Native PAGE (polyacrylamide gel electrophoresis) of PO showed the single isoform in all the treatment including the control and difference is by the increased intensity of the band in the inoculated control and FP 7 treatment in the tomato plant. Isoform analysis of the PPO showed the induction of the PPO in the P. fluorescens treated plants challenged with P. aphanidermatum. -1,3 glucanase in tomato cultivar, Co 3 with and without challenge inoculation of P. aphanidermatum, revealed changes in the isoform pattern after staining the gel with 2,3,5-triphenyl tetrazolium chloride. Moreover, higher accumulation of phenolics was noticed in plants pretreated with P. fluorescens isolate FP 7 challenged with P. aphanidermatum. The relevant function of Thaumatin like defense proteins and secondary metabolites involved in the phenylpropanoid pathway collectively contributing to enhanced resistance is discussed.