Sesame is a major cooking oil crop in Korea. One of the primary problems in sesame cultivation is low healthy stand establishment due to the occurrence of seedling rot and damping-off resulting from a complex of soil-borne pathogens in the field. To address the problem, the bioformulation of Pseudomonas fluorescens M45 was prepared in powder form using clay and vermiculite, and was evaluated for its effect on biological control of soil-borne pathogens in sesame cultivation. In the petri dish trial, the emergence rate was overall good (> 92%) regardless of seeds being pelleted and/or M45-treated. In both pot and field trials containing disease-conducive soils, seed-pelleting substantially reduced emergence rate, whereas seed-pelleting with M45 significantly improved the emergence rate (> 26%). The emergence rate of sesame seeds treated with the strain M45 was greater than 30% regardless of seed pelletization. We also found that M45r colonized in the roots at the density of 1.6×105 cfu/g. With aid of the bioformulation, however, root colonization of the strain was significantly increased to 4.0×106 cfu/g. The powder formulation with strain M45 enhanced the rate of healthy stand establishment in disease-conducive soil. Therefore, bioformulation with strain M45 is a promising method to overcome problems associated with the successive cultivation of sesame.