The aim of this study was to evaluate in vitro the efficacy of clinically using colistin methanesulfonate against biofilm-forming multidrug-resistant Pseudomonas aeruginosa (MDRP), with minimum inhibitory concentrations (MICs) of ciprofloxacin, imipenem, and amikacin showing ≥4, 16, and 32 μg/ml, respectively, by disk diffusion susceptibility testing (CLSI document M100-S21). The minimum eradication biofilm concentration (MBEC) of colistin methanesulfonate for strain MDRP-YMD isolated from a patient's urine, which formed a biofilm on plastic pegs attached to a microplate lid, was compared with that of P. aeruginosa ATCC27853 for quality control testing with MICs of ciprofloxacin, imipenem, and amikacin showing ≤1, 4, and 16 μg/ml, respectively. In an uneven biofilm approximately 10 μm thick, as determined with confocal laser scanning microscopy (CLSM), ratios of MBEC to MIC of colistin methanesulfonate against strains MDRP-YMD and ATCC27853 were 10.5 and 8.0, whereas those of minimum bactericidal concentration (MBC) to MIC in planktonic cells were 1.0 and 2.0 μg/ml, respectively. Morphological examination using scanning electron microscopy and CLSM verified that embedded cells in biofilm matrices of the two strains were disrupted and died under the MBEC. Therefore, bactericidal effects of colistin methanesulfonate on biofilm-forming cells of strain MDRP-YMD as well as strain ATCC27853 were significantly decreased compared with those on the planktonic cells.