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Fusarium wilt is one of the major constraints on cucumber production worldwide. Several strategies have been used to control the causative pathogen, Fusarium oxysporum f. sp. cucumerinum J. H. Owen, including soil solarization, fungicide seed treatment and biological control. In this study, F. oxysporum f. sp. cucumerinum was successfully controlled by a newly isolated strain, Bacillus subtilis SQR 9, in vitro and in vivo. Greenhouse experiments were carried out to evaluate the effect of inoculation and solid fermentation of organic fertilizer with B. subtilis SQR 9, hereby defined as bio-organic fertilizer (BIO), on the control of Fusarium wilt. In comparison with the control, the wilt incidence was significantly reduced (49-61% reduction) by application of BIO. The rhizosphere population of F. oxysporum f. sp. cucumerinum, as detected both by selective plating and realtime PCR, was significantly lower in BIO-treated plants than the control. The localization of bacterial cells, pattern of colonization and survival of B. subtilis SQR 9 in the rhizsosphere of cucumber, was examined by fluorescent microscopy and explored following recovery of the green fluorescent protein ( gfp)-labeled SQR 9 with the new gfp-marked shuttle vector pHAPII through selective plating. The preferential sites of the labeled strain were the differentiation and elongation zone, root hair and the lateral root junctions. The population of the strain was 10 cfu/g root in rhizoplane. These results indicate that the strain was able to survive well in the rhizosphere of cucumber, suppressed growth of F. oxysporum in the rhizosphere of cucumber and protected the host from the pathogen. [ABSTRACT FROM AUTHOR]