Abstract: Pseudomonas fluorescens GcM5-1A carried by pine wood nematodes was cultured in LB, NB and PD medium. The cultures free of bacteria were used to analyze their toxicity to suspension cells and shoot seedlings of Pinus thunbergii. The cultures of LB and NB were toxic, with LB culture showing the highest toxicity, whereas almost no toxicity was detected for PD culture. pH values of the LB medium affected the toxicity of the final culture: the culture with an initial pH 7.0 was more toxic than one with pH 5.0. The proteins in the LB culture were precipitated by ammonium sulfate, and toxicity analysis showed the proteins toxic to both suspension cells and seedlings. As well, a component mainly containing a protein of 50 kDa, which also showed relatively strong toxicity, was partially purified on precipitation with ammonium sulfate of 20% saturation; treatment with the component could lead to leakage of soluble carbohydrates and free amino acids.