Organic farming systems can effectively control the pathogens that cause plant diseases. When rice seedlings inoculated with Burkholderia glumae at germination were cultivated on each of three independent organic soils supplied by organic growers, or on conventional soil as a control, development of seedling rot symptoms was significantly suppressed on all organic soils, but not on conventional soil. This disease-suppressive activity of the organic soils was also observed for rice seedling damping-off disease caused by Burkholderia plantarii. Interestingly, such disease suppression was completely compromised on organic soils sterilized at 121 °C, indicating biological activity included in organic soils seems to be associated with the suppression of rice seedling diseases. To explore the putative biological factor(s) conferring the disease-suppressive activity of organic soils, we isolated bacteria from the filtrates of organic soil suspensions. Among these filtrates, two bacterial isolates could suppress development of bacterial seedling rot symptoms, whereas Escherichia coli as a control could not. The 16S rDNA and rpoD nucleotide fragment sequences of two bacterial isolates conferring the observed disease-suppressive activity were highly homologous to those of Pseudomonas sp. Furthermore, phylogenetic analysis of these nucleotide sequences suggested that two isolates placed in the P. fluorescens group. These results reveal that certain Pseudomonas sp. that inhabit organic soils likely play a role in the suppression of rice seedling diseases in organic farming systems.