The early stage of plant-rhizobacteria interaction, affected by plant root exudates and plant-rhizobacteria surface contact, is considered to be critical for plant growth-promoting rhizobacteria colonizing plant roots and initiating the beneficial effects on plant growth. However, little is known about the mechanisms of plant-rhizobacteria surface contact involved in early stage of plant-rhizobacteria interaction. In order to reveal the molecular mechanisms of the surface contact, a rhizobacterium Bacillus amyloliquefaciens B55 was interacted with plant roots of rice R109 and used to perform a cDNA-based suppression-subtractive hybridization. Seven differentially expressed DNA fragments were identified. Except for the two fragments showing no matches to any known sequences in the Genbank, the other five fragments were found to have high homologies with the genes encoding 2-oxoglutarate dehydrogenase E1 component OdhA, aspartate ammonia-lyase AnsB, and hypothetical protein proposed to be involved in surface adhesion, acetolactate decarboxylase AlsD, and DNA mismatch repair protein MutL, respectively. The induced RNA expression levels of two putative genes ansB and odhA and an unmatched DNA fragment BD33 were verified by RT-PCR analysis.